cqm-parsers 0.2.1 → 0.2.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -1,8 +1,7 @@
-source "https://rubygems.org"
+source 'https://rubygems.org'
 
 gemspec :development_group => :test
 
-gem 'mustache'
 gem 'cqm-models', '~> 0.8.4'
 gem 'mongoid', '~> 5.0.0'
 
@@ -18,12 +17,14 @@ end
 
 group :test do
   gem 'factory_girl', '~> 4.1.0'
-  gem "tailor", '~> 1.1.2'
-  gem "cane", '~> 2.3.0'
+  gem 'tailor', '~> 1.1.2'
+  gem 'cane', '~> 2.3.0'
+  gem 'codecov'
   gem 'simplecov', :require => false
   gem 'webmock'
   gem 'minitest', '~> 5.3'
   gem 'minitest-reporters'
   gem 'awesome_print', :require => 'ap'
   gem 'simplexml_parser', :git => 'https://github.com/projecttacoma/simplexml_parser.git', :branch => 'master'
+  gem 'vcr'
 end

data/README.md

@@ -1,3 +1,6 @@
+[![codecov](https://codecov.io/gh/projecttacoma/cqm-parsers/branch/master/graph/badge.svg)](https://codecov.io/gh/projecttacoma/cqm-parsers)
+
+
 cqm-parsers
 ===========
 

data/Rakefile

@@ -1,6 +1,5 @@
 require 'rake/testtask'
 require 'cane/rake_task'
-require "simplecov"
 
 import 'lib/tasks/hqmf.rake'
 

data/lib/hqmf-model/data_criteria.json

@@ -647,6 +647,15 @@
       "hard_status":false,
       "patient_api_function":"communications",
       "not_supported":false},
+  "communication_performed":{
+      "title":"communication, performed",
+      "category":"communications",
+      "definition":"communication",
+      "status":"performed",
+      "sub_category":"",
+      "hard_status":false,
+      "patient_api_function":"communications",
+      "not_supported":false},
   "device":{
       "title":"device",
       "category":"devices",
@@ -1007,6 +1016,15 @@
       "hard_status":false,
       "patient_api_function":"encounters",
       "not_supported":false},
+  "assessment_ordered":{
+      "title":"assessment order",
+      "category":"assessments",
+      "definition":"assessment",
+      "status":"ordered",
+      "sub_category":"",
+      "hard_status":false,
+      "patient_api_function":"assessments",
+      "not_supported":false},
   "assessment_performed":{
       "title":"assessment performed",
       "category":"assessments",
@@ -1042,5 +1060,14 @@
       "sub_category":"",
       "hard_status":false,
       "patient_api_function":"allergies",
+      "not_supported":false},
+  "participation":{
+      "title":"participation",
+      "category":"participations",
+      "definition":"participation",
+      "status":"",
+      "sub_category":"",
+      "hard_status":false,
+      "patient_api_function":"participations",
       "not_supported":false}
 }

data/lib/hqmf-model/data_criteria.rb

@@ -24,24 +24,35 @@ module HQMF
     # `code`: The code for the entry. This should be included to make HQMF generation work properly. This is whatever code is dictated in the HQMF. For Diagnosis, this is in [HQMF QDM IG](http://www.hl7.org/implement/standards/product_brief.cfm?product_id=346) vol 2 page 155 and is `29308-4`.
     # `code_system`: This is the oid for whatever code system contains `code`. For Diagnosis, this is LOINC: `2.16.840.1.113883.6.1`. This is also located at (http://www.hl7.org/implement/standards/product_brief.cfm?product_id=346) vol 2 page 155.
     # `template_id`: These appear to be related to HQMFr1 template ids. These appear to be dangerously out of date. Don't use.
-    FIELDS = {'ABATEMENT_DATETIME' => {title:'Abatement Datetime', coded_entry_method: :end_date, field_type: :timestamp},
-              'ACTIVE_DATETIME' => {title:'Active Date/Time', coded_entry_method: :active_date_time, field_type: :timestamp},
+    FIELDS = {'ABATEMENT_DATETIME' => {title:'Abatement Datetime', coded_entry_method: :end_date, field_type: :timestamp}, # ABATEMENT_DATETIME is no longer used.
+              'ACTIVE_DATETIME' => {title:'Active Date/Time', coded_entry_method: :active_datetime, field_type: :timestamp},
+              # ADMISSION_DATETIME is no longer used.
               'ADMISSION_DATETIME' => {title:'Admission Date/Time', coded_entry_method: :admit_time, code: '399423000', code_system:'2.16.840.1.113883.6.96', field_type: :timestamp},
               # QDM 5.0 addition. This is the same as FACILITY_LOCATION.
               # TODO: (LDY 10/5/2016) this is a new attribute from QDM 5.0. We do not yet have the code or template_id for this. This should be updated when we do.
               'ADMISSION_SOURCE' => {title:'Admission Source', coded_entry_method: :admission_source, field_type: :value},
+              # ANATOMICAL_APPROACH_SITE is no longer used.
               'ANATOMICAL_APPROACH_SITE' => {title:'Anatomical Approach Site', coded_entry_method: :anatomical_approach,  field_type: :value},
               'ANATOMICAL_LOCATION_SITE' => {title:'Anatomical Location Site', coded_entry_method: :anatomical_location,  field_type: :value},
+              # ANATOMICAL_STRUCTURE is no longer used.
               'ANATOMICAL_STRUCTURE' => {title:'Anatomical Structure', coded_entry_method: :anatomical_structure, code: '91723000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1000.2', field_type: :value},
+              # Added in QDM 5.4
+              'CATEGORY' => {title:'Category', coded_entry_method: :category, field_type: :value},
               'CAUSE' => {title:'Cause', coded_entry_method: :cause_of_death, code: '42752001', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1017.2', field_type: :value},
               # TODO: Determine actual code and code_system for component attribute
               'COMPONENT' => {title: 'Component', coded_entry_method: :components, field_type: :value},
+              # CUMULATIVE_MEDICATION_DURATION is no longer used.
               'CUMULATIVE_MEDICATION_DURATION' => {title:'Cumulative Medication Duration', coded_entry_method: :cumulative_medication_duration, code: '261773006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1001.3', field_type: :value},
               # MISSING Date - The date that the patient passed away. - Patient Characteristic Expired
+              # Could not find a code and code_system for this data criteria (days supplied) in HQMF QDM IG v3
+              'DAYS_SUPPLIED' => {title:'Days Supplied', coded_entry_method: :days_supplied, field_type: :value},
               'DIAGNOSIS' => {title:'Diagnosis', coded_entry_method: :diagnosis, field_type: :value},
+              # DISCHARGE_DATETIME is no longer used.
               'DISCHARGE_DATETIME' => {title:'Discharge Date/Time', coded_entry_method: :discharge_time, code: '442864001', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1025.1', field_type: :timestamp},
               # TODO: (LDY 10/5/2016) this changed from "discharge status" to "discharge disposition". likely there is a code and template id change necessary. these are not yet known.
+              # DISCHARGE_STATUS is no longer used.
               'DISCHARGE_STATUS' => {title:'Discharge Disposition', coded_entry_method: :discharge_disposition, code: '309039003', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1003.2', field_type: :value},
+              'DISPENSER_IDENTIFIER' => {title:'Dispenser Identifier', coded_entry_method: :dispenser_identifier, field_type: :value},
               # TODO: (LDY 10/4/2016) this changed from "dose" to "dosage". it's possible that there's another code associated with this. this code was not available at the time of this change.
               'DOSE' => {title:'Dosage', coded_entry_method: :dose, code: '398232005', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1004.1', field_type: :value},
               'FACILITY_LOCATION' => {title:'Facility Location', coded_entry_method: :facility, code: 'SDLOC', field_type: :value},
@@ -49,49 +60,72 @@ module HQMF
               'FACILITY_LOCATION_ARRIVAL_DATETIME' => {title:'Location Period Start Date/Time', coded_entry_method: :facility_arrival, code: 'SDLOC_ARRIVAL', field_type: :nested_timestamp},
               'FACILITY_LOCATION_DEPARTURE_DATETIME' => {title:'Location Period End Date/Time', coded_entry_method: :facility_departure, code: 'SDLOC_DEPARTURE', field_type: :nested_timestamp},
               'FREQUENCY' => {title:'Frequency', coded_entry_method: :administration_timing, code: '307430002', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1006.1', field_type: :value},
+              # HEALTH_RECORD_FIELD is no longer used.
               'HEALTH_RECORD_FIELD' => {title: 'Health Record Field', coded_entry_method: :health_record_field, code: '395676008', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.28.3.102:2014-11-24', field_type: :value},
               'INCISION_DATETIME' => {title:'Incision Date/Time', coded_entry_method: :incision_time, code: '34896006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.89', field_type: :timestamp},
+              # LATERALITY is no longer used.
               'LATERALITY' => {title:'Laterality', coded_entry_method: :laterality, code: '272741003', code_system:'2.16.840.1.113883.6.96', template_id: '', field_type: :value},
               'LENGTH_OF_STAY' => {title:'Length of Stay', coded_entry_method: :length_of_stay, code: '183797002', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1029.3', field_type: :value},
+              # Added in QDM 5.4
+              'MEDIUM' => {title:'Medium', coded_entry_method: :medium, field_type: :value},
               'METHOD' => {title:'Method', coded_entry_method: :method, template_id: '', field_type: :value},
               # Negation Rationale isn't encoded
+              # ONSET_AGE is no longer used.
               'ONSET_AGE' => {title:'Onset Age', coded_entry_method: :onset_age, code: '445518008', code_system:'2.16.840.1.113883.6.96', template_id: '', field_type: :value},
+              # ONSET_DATETIME is no longer used.
               'ONSET_DATETIME' => {title:'Onset Datetime', coded_entry_method: :start_date, field_type: :timestamp},
+              # ORDINAL is no longer used.
               'ORDINAL' => {title:'Ordinality', coded_entry_method: :ordinality, code: '117363000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1012.2', field_type: :value}, # previous
               'ORDINALITY' => {title:'Ordinality', coded_entry_method: :ordinality, code: '117363000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1012.2', field_type: :value},
+              # PATIENT_PREFERENCE is no longer used.
               'PATIENT_PREFERENCE' => {title:'Patient Preference', coded_entry_method: :patient_preference,  code: 'PAT', code_system: '2.16.840.1.113883.5.8', template_id: '2.16.840.1.113883.10.20.24.3.83', field_type: :value},
+              'PRESCRIBER_IDENTIFIER' => {title:'Prescriber Identifier', coded_entry_method: :prescriber_identifier, field_type: :value},
               'PRINCIPAL_DIAGNOSIS' => {title:'Principal Diagnosis', coded_entry_method: :principal_diagnosis, field_type: :value},
+              # PROVIDER_PREFERENCE is no longer used.
               'PROVIDER_PREFERENCE' => {title:'Provider Preference', coded_entry_method: :provider_preference, code: '103323008', code_system: '2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.84', field_type: :value},
+              # RADIATION_DOSAGE is no longer used.
               'RADIATION_DOSAGE' => {title:'Radiation Dosage', coded_entry_method: :radiation_dose, code: '228815006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.91', field_type: :value},
+              # RADIATION_DURATION is no longer used.
               'RADIATION_DURATION' => {title:'Radiation Duration', coded_entry_method: :radiation_duration, code: '306751006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.91', field_type: :value},
+              # REACTION is no longer used.
               'REACTION'=> {title:'Reaction', coded_entry_method: :reaction, code: '263851003', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.85', field_type: :value},
               'REASON' => {title:'Reason', coded_entry_method: :reason, code: '410666004', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.88', field_type: :value},
+              # Added in QDM 5.4
+              'RECIPIENT' => {title:'Recipient', coded_entry_method: :recipient, field_type: :value},
+              # RECORDED_DATETIME is no longer used.
               'RECORDED_DATETIME' => {title:'Recorded Datetime', coded_entry_method: :start_date, field_type: :timestamp},
               'REFERENCE_RANGE_HIGH' => {title:'Reference Range - High', coded_entry_method: :reference_range_high, field_type: :value},
               'REFERENCE_RANGE_LOW' => {title:'Reference Range - Low', coded_entry_method: :reference_range_low, field_type: :value},
               'REFILLS' => {title:'Refills', coded_entry_method: :refills,  field_type: :value},
               'RELATED_TO' => {title:'Related To', coded_entry_method: :related_to,  code: 'REL', codeSystem: '2.16.840.1.113883.1.11.11603', field_type: :value},
               'RELATIONSHIP' => {title:'Relationship', coded_entry_method: :relationship_to_patient, field_type: :value},
+              # REMOVAL_DATETIME is no longer used.
               'REMOVAL_DATETIME' => {title:'Removal Date/Time', coded_entry_method: :removal_time, code: '118292001', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1032.1', field_type: :timestamp},
               # Result isn't encoded
               # TODO: (LDY 10/4/2016) RESULT_DATETIME is a new attribute in QDM 5.0. We do not yet have codes/template information for this.
               'RESULT_DATETIME' => {title:'Result Date/Time', coded_entry_method: :result_date_time, field_type: :timestamp},
               'ROUTE' => {title:'Route', coded_entry_method: :route, code: '263513008', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1020.2', field_type: :value},
+              # Added in QDM 5.4
+              'SENDER' => {title:'Sender', coded_entry_method: :sender, field_type: :value},
+              'SETTING' => {title:'Setting', coded_entry_method: :setting, field_type: :value},
               'SEVERITY' => {title:'Severity', coded_entry_method: :severity, code: 'SEV', code_system:'2.16.840.1.113883.5.4', template_id: '2.16.840.1.113883.10.20.22.4.8', field_type: :value},
+              # SIGNED_DATETIME is no longer used.
               'SIGNED_DATETIME' =>  {title:'Signed Date/Time', coded_entry_method: :signed_date_time, field_type: :timestamp},
+              # START_DATETIME is no longer used.
               'START_DATETIME' => {title:'Start Date/Time', coded_entry_method: :start_date, code: '398201009', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1027.1', field_type: :timestamp},
               # STATUS is referenced in the code as `qdm_status` because entry/Record already has a `status`/`status_code` field which has a different meaning
               'STATUS' => {title: 'Status', coded_entry_method: :qdm_status, code: '33999-4', code_system:'2.16.840.1.113883.6.1', field_type: :value},
+              # STOP_DATETIME is no longer used.
               'STOP_DATETIME' => {title:'Stop Date/Time', coded_entry_method: :end_date, code: '397898000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1026.1', field_type: :timestamp},
               # TODO: (LDY 10/4/2016) SUPPLY is a new attribute in QDM 5.0. We do not yet have codes/template information for this.
               'SUPPLY' => {title:'Supply', coded_entry_method: :supply, field_type: :value},
               'TARGET_OUTCOME' => {title:'Target Outcome', coded_entry_method: :target_outcome, code: '385676005', code_system:'2.16.840.1.113883.6.96', template_id: '', field_type: :value},
-              # MISSING Time - The time that the patient passed away
 
               # Custom field values
               # QDM 5.3 Update: "Related To" replaces Fulfills. We are keeping the fulfills code and only make changes to the UI.
               'FLFS' => {title:'Related To', coded_entry_method: :fulfills, code: 'FLFS', field_type: :reference},
               'SOURCE' => {title:'Source', coded_entry_method: :source, code: '260753009', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.2001.2', field_type: :value},
+              # TRANSFER_FROM, TRANSFER_FROM_DATETIME, TRANSFER_TO, and TRANSFER_TO_DATETIME are no longer used.
               'TRANSFER_FROM' => {title:'Transfer From', coded_entry_method: :transfer_from, code: 'TRANSFER_FROM', template_id: '2.16.840.1.113883.10.20.24.3.81', field_type: :value},
               'TRANSFER_FROM_DATETIME' => {title:'Transfer From Date/Time', coded_entry_method: :transfer_from_time, code: 'ORG_TIME', template_id: '2.16.840.1.113883.10.20.24.3.81', field_type: :nested_timestamp},
               'TRANSFER_TO' => {title:'Transfer To', coded_entry_method: :transfer_to, code: 'TRANSFER_TO', template_id: '2.16.840.1.113883.10.20.24.3.82', field_type: :value},
@@ -455,6 +489,10 @@ module HQMF
           value = HQMF::Collection.from_json(json)
         when 'FAC'
           value = Facility.new(json)
+        when 'ID'
+          value = HQMF::Identifier.from_json(json)
+        when 'RT'
+          value = HQMF::Ratio.from_json(json)
         else
           raise "Unknown value type [#{type}]"
         end
@@ -463,5 +501,4 @@ module HQMF
 
 
   end
-
 end

data/lib/hqmf-model/types.rb

@@ -453,5 +453,42 @@ module HQMF
       check_equality(self,other)
     end
   end
+
+  class Ratio
+    include HQMF::Conversion::Utilities
+    attr_accessor :type, :numerator, :denominator
+
+    # @param [String] type
+    # @param [Value] numerator
+    # @param [Value] denominator
+    def initialize(type, numerator, denominator)
+      @type = type || 'RT'
+      @numerator = numerator
+      @denominator = denominator
+    end
+
+    def self.from_json(json)
+      type = json["type"] if json["type"]
+      numerator = json["numerator"] if json["numerator"]
+      denominator = json["denominator"] if json["denominator"]
+      HQMF::Ratio.new(type, numerator, denominator)
+    end
+
+    def numerator?
+      @numerator
+    end
+
+    def denominator?
+      @denominator
+    end
+
+    def to_json
+      build_hash(self, [:type, :numerator, :denominator])
+    end
+
+    def ==(other)
+      check_equality(self, other)
+    end
+  end
   
 end

data/lib/hqmf-parser/2.0/document.rb

@@ -192,7 +192,7 @@ module HQMF2
       value_obj = handle_attribute_value(attribute, value) if attribute.at_xpath('./cda:value', NAMESPACES)
 
       # Handle the cms_id - changed to eCQM in MAT 5.4 (QDM 5.3)
-      @cms_id = "CMS#{value}v#{@hqmf_version_number.to_i}" if (name.include? 'eMeasure Identifier') || (name.include? 'eCQM Identifier')
+      @cms_id = "CMS#{value}v#{@hqmf_version_number.to_i}" if (!name.nil?) && ((name.include? 'eMeasure Identifier') || (name.include? 'eCQM Identifier'))
 
       HQMF::Attribute.new(id, code, value, nil, name, id_obj, code_obj, value_obj)
     end

data/lib/hqmf-parser/2.0/document_helpers/doc_population_helper.rb

@@ -32,24 +32,17 @@ module HQMF2
     # Returns the population descriptions and criteria found in this document
     def extract_populations_and_criteria
       has_observation = extract_observations
-      document_populations = @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection',
-                                        HQMF2::Document::NAMESPACES)
-      # Sort the populations based on the id/extension, since the populations may be out of order; there doesn't seem to
-      # be any other way that order is indicated in the HQMF
-      document_populations = document_populations.sort_by do |pop|
-        pop.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES).try(:value)
-      end
+      document_populations = get_document_populations
       number_of_populations = document_populations.length
       document_populations.each_with_index do |population_def, population_index|
         population = {}
         handle_base_populations(population_def, population)
 
-        id_def = population_def.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES)
-        population['id'] = id_def ? id_def.value : "Population#{population_index}"
-        title_def = population_def.at_xpath('cda:title/@value', HQMF2::Document::NAMESPACES)
-        population['title'] = title_def ? title_def.value : "Population #{population_index}"
+        id_def = get_id_def(population_def)
+        add_id_to_population(id_def, population, population_index)
+        add_title_to_population(population_def, population)
+        add_observ_to_population(has_observation, population)
 
-        population['OBSERV'] = 'OBSERV' if has_observation
         @populations << population
         handle_stratifications(population_def, number_of_populations, population, id_def, population_index)
       end
@@ -59,6 +52,37 @@ module HQMF2
       [@populations, @population_criteria]
     end
 
+    def get_document_populations
+      document_populations = @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection',
+                                        HQMF2::Document::NAMESPACES)
+      # Sort the populations based on the id/extension, since the populations may be out of order; there doesn't seem to
+      # be any other way that order is indicated in the HQMF
+      document_populations.sort_by do |pop|
+        pop.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES).try(:value)
+      end
+    end
+
+    def get_id_def(population_def)
+      population_def.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES)
+    end
+
+    def get_title_def(population_def)
+      population_def.at_xpath('cda:title/@value', HQMF2::Document::NAMESPACES)
+    end
+
+    def add_id_to_population(id_def, population, population_index)
+      population['id'] = id_def ? id_def.value : "Population#{population_index}"
+    end
+
+    def add_title_to_population(population_def, population)
+      title_def = get_title_def(population_def)
+      population['title'] = title_def ? title_def.value : "Population #{population_index}"
+    end
+
+    def add_observ_to_population(has_observation, population)
+      population['OBSERV'] = 'OBSERV' if has_observation
+    end
+
     # Extracts the measure observations, will return true if one exists
     def extract_observations
       has_observation = false

data/lib/hqmf-parser/2.0/value_set_helper.rb

@@ -92,8 +92,8 @@ module HQMF2
       '2.16.840.1.113883.10.20.28.3.117' => { valueset_path: './*/cda:code', result_path: './*/cda:value' },
       '2.16.840.1.113883.10.20.28.3.118' => { valueset_path: './*/cda:code', result_path: nil },
       '2.16.840.1.113883.10.20.28.3.119' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingEntity[@classCode='MMAT']/cda:code", result_path: nil },
-      '2.16.840.1.113883.10.20.28.3.120' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingEntity[@classCode='MMAT']/cda:code", result_path: nil }
-
+      '2.16.840.1.113883.10.20.28.3.120' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingEntity[@classCode='MMAT']/cda:code", result_path: nil },
+      '2.16.840.1.113883.10.20.28.3.130' => { valueset_path: './*/cda:value', result_path: nil }
     }
     # rubocop:enable Metrics/LineLength
 

data/lib/hqmf-parser/cql/document_helpers/doc_population_helper.rb

@@ -40,7 +40,11 @@ module HQMF2CQL
           # The at_xpath(...).values returns an array of a single element.
           # The match returns an array and since we don't want the double quotes we take the second element
           cql_define_function[:function_name] = entry.at_xpath("*/cda:measureObservationDefinition/cda:value/cda:expression").values.first.match('\\"([A-Za-z0-9 ]+)\\"')[1]
-          cql_define_function[:parameter] = entry.at_xpath("*/cda:measureObservationDefinition/cda:component/cda:criteriaReference/cda:id").attributes['extension'].value.match('\\"([A-Za-z0-9 ]+)\\"')[1]
+          # The criteria_reference_id is the id of the measurePopulationCriteria that should be used for this observation function
+          measure_population_id = entry.at_xpath("*/cda:measureObservationDefinition/cda:component/cda:criteriaReference/cda:id").attributes['root'].value
+          # Get the name of the parameter to the  observation function within the measurePopulationCriteria section
+          cql_define_function[:parameter] = @doc.at_xpath("cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection/cda:component/cda:measurePopulationCriteria/cda:id[@root = \"#{measure_population_id}\"]/../cda:precondition/cda:criteriaReference/cda:id").attributes['extension'].value.match('\\"([A-Za-z0-9 ]+)\\"')[1]
+
           @observations << cql_define_function
         end
       end
@@ -120,5 +124,45 @@ module HQMF2CQL
       end
     end
 
+    # Returns the population descriptions and criteria found in this document
+    def extract_populations_and_criteria
+      has_observation = extract_observations
+      document_populations = get_document_populations
+      number_of_populations = document_populations.length
+      document_populations.each_with_index do |population_def, population_index|
+        population = {}
+        handle_base_populations(population_def, population)
+
+        id_def = get_id_def(population_def)
+        add_id_to_population(id_def, population, population_index)
+        add_title_to_population(population_def, population)
+        add_observ_to_population(has_observation, population)
+
+        add_supplemental_data_elements_to_population(population_def, population)
+
+        @populations << population
+        handle_stratifications(population_def, number_of_populations, population, id_def, population_index)
+      end
+
+      # Push in the stratification populations after the unstratified populations
+      @populations.concat(@stratifications)
+      [@populations, @population_criteria]
+    end
+
+    def add_supplemental_data_elements_to_population(population_def, population)
+      begin
+        supplemental_data_elements_def = population_def.xpath('cda:component/cql-ext:supplementalDataElement')
+      rescue Nokogiri::XML::XPath::SyntaxError
+        # Older fixtures without SDEs don't have the cql-ext namespace
+        return
+      end
+
+      supplemental_data_elements = []
+      supplemental_data_elements_def.each do |sde_def|
+        cql_definition_name = sde_def.at_xpath('cda:precondition/cda:criteriaReference/cda:id').attribute('extension').to_s.match(/"([^"]*)"/)[1]
+        supplemental_data_elements << cql_definition_name
+      end
+      population['supplemental_data_elements'] = supplemental_data_elements
+    end
   end
 end

data/lib/hqmf-parser/cql/value_set_helper.rb

@@ -75,7 +75,7 @@ module HQMF2CQL
       '2.16.840.1.113883.10.20.28.4.75' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='ADMM']/cda:playingMaterial[@classCode='MAT' and @determinerCode='KIND']/cda:code", result_path: nil },
       '2.16.840.1.113883.10.20.28.4.76' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='ADMM']/cda:playingMaterial[@classCode='MAT' and @determinerCode='KIND']/cda:code", result_path: nil },
       '2.16.840.1.113883.10.20.28.4.77' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='ADMM']/cda:playingMaterial[@classCode='MAT' and @determinerCode='KIND']/cda:code", result_path: nil },
-      '2.16.840.1.113883.10.20.28.4.78' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingMaterial[@classCode='MMAT' and @determinerCode='KIND']/cda:code", result_path: nil },
+      '2.16.840.1.113883.10.20.28.4.78' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='ADMM']/cda:playingMaterial[@classCode='MAT' and @determinerCode='KIND']/cda:code", result_path: nil },
       '2.16.840.1.113883.10.20.28.4.79' => { valueset_path: './*/cda:value', result_path: nil },
       '2.16.840.1.113883.10.20.28.4.80' => { valueset_path: './*/cda:value', result_path: nil },
       '2.16.840.1.113883.10.20.28.4.81' => { valueset_path: './*/cda:value', result_path: nil },
@@ -92,7 +92,10 @@ module HQMF2CQL
       '2.16.840.1.113883.10.20.28.4.117' => { valueset_path: './*/cda:code', result_path: './*/cda:value' },
       '2.16.840.1.113883.10.20.28.4.118' => { valueset_path: './*/cda:code', result_path: nil },
       '2.16.840.1.113883.10.20.28.4.119' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingEntity[@classCode='MMAT']/cda:code", result_path: nil },
-      '2.16.840.1.113883.10.20.28.4.120' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingEntity[@classCode='MMAT']/cda:code", result_path: nil }
+      '2.16.840.1.113883.10.20.28.4.120' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingEntity[@classCode='MMAT']/cda:code", result_path: nil },
+      '2.16.840.1.113883.10.20.28.4.130' => { valueset_path: './*/cda:value', result_path: nil },
+      '2.16.840.1.113883.10.20.28.4.131' => { valueset_path: './*/cda:code', result_path: nil },
+      '2.16.840.1.113883.10.20.28.4.132' => { valueset_path: "./*/cda:outboundRelationship[@typeCode='RSON']/cda:observationCriteria/cda:value", result_path: nil }
     }
     # rubocop:enable Metrics/LineLength
 

data/lib/qrda-export/catI-r5/qrda_header/_record_target.mustache

@@ -1,6 +1,5 @@
 <recordTarget>
   <patientRole>
-    <id extension="{{mrn}}" root="Bonnie"/>
     <id extension="{{mrn}}" root="1.3.6.1.4.1.115" />
     <addr use="HP">
       <streetAddressLine>202 Burlington Rd.</streetAddressLine>

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

@@ -9,12 +9,12 @@
     {{#relevantPeriod}}
     {{{relevant_period}}}
     {{/relevantPeriod}}
+    {{#result}}
+    {{{result_value}}}
+    {{/result}}
     {{#authorDatetime}}
     {{> qrda_templates/template_partials/_author}}
     {{/authorDatetime}}
-    {{#result}}
-    {{> qrda_templates/template_partials/_results}}
-    {{/result}}
     {{#negationRationale}}
     {{> qrda_templates/template_partials/_reason}}
     {{/negationRationale}}

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

@@ -1,7 +1,6 @@
 <entry>
   <act classCode="ACT" moodCode="RQO" {{{negation_ind}}}>
     <templateId root="2.16.840.1.113883.10.20.24.3.132" extension="2017-08-01"/>
-    <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <code code="ENC" codeSystem="2.16.840.1.113883.5.6" displayName="Encounter" codeSystemName="ActClass"/>
     <entryRelationship typeCode="SUBJ">
       <encounter classCode="ENC" moodCode="RQO">

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

@@ -2,7 +2,6 @@
   <act classCode="ACT" moodCode="EVN">
     <!--Encounter performed Act -->
     <templateId extension="2017-08-01" root="2.16.840.1.113883.10.20.24.3.133"/>
-    <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="EVN">

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

@@ -4,6 +4,7 @@ module QRDA
   
       def initialize(entry_finder = nil)
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
         @relevant_period_xpath = "./cda:effectiveTime"
         @author_datetime_xpath = "./cda:author/cda:time"

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

@@ -38,8 +38,8 @@ module QRDA
 
       def create_entry(entry_element, _nrh = NarrativeReferenceHandler.new)
         entry = @entry_class.new
-        @entry_id_map[extract_id(entry_element, "./cda:id").value] ||= []
-        @entry_id_map[extract_id(entry_element, "./cda:id").value] << entry.id
+        @entry_id_map[extract_id(entry_element, @id_xpath).value] ||= []
+        @entry_id_map[extract_id(entry_element, @id_xpath).value] << entry.id
         entry.dataElementCodes = extract_codes(entry_element, @code_xpath)
         extract_dates(entry_element, entry)
         if @result_xpath

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

@@ -3,6 +3,7 @@ module QRDA
     class AdverseEventImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.146']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:entryRelationship/cda:observation/cda:value'
         @author_datetime_xpath = './cda:author/cda:time'
         @relevant_period_xpath = './cda:effectiveTime'

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

@@ -3,6 +3,7 @@ module QRDA
     class AllergyIntoleranceImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.147']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:participant/cda:participantRole/cda:playingEntity/cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @prevalence_period_xpath = "./cda:effectiveTime"

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

@@ -3,9 +3,10 @@ module QRDA
     class AssessmentPerformedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.144']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
-        @result_xpath = "./cda:value | ./cda:entryRelationship[@typeCode='REFR']/cda:observation/cda:value"
+        @result_xpath = "./cda:value"
         @method_xpath = './cda:methodCode'
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
         @entry_class = QDM::AssessmentPerformed

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

@@ -3,6 +3,7 @@ module QRDA
     class CommunicationFromPatientToProviderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.2']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @entry_class = QDM::CommunicationFromPatientToProvider

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

@@ -3,6 +3,7 @@ module QRDA
     class CommunicationFromProviderToPatientImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.3']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @entry_class = QDM::CommunicationFromProviderToPatient

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

@@ -3,6 +3,7 @@ module QRDA
     class CommunicationFromProviderToProviderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @related_to_xpath = "./sdtc:inFulfillmentOf1/sdtc:actReference"

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

@@ -3,6 +3,7 @@ module QRDA
     class DeviceAppliedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.7']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:participant/cda:participantRole/cda:playingDevice/cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @relevant_period_xpath = "./cda:effectiveTime"

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

@@ -3,6 +3,7 @@ module QRDA
     class DeviceOrderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.130']"))
         super(entry_finder)
+        @id_xpath = './cda:entryRelationship/cda:supply/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.9']/cda:participant/cda:participantRole/cda:playingDevice/cda:code"
         @author_datetime_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.9']/cda:author/cda:time"
         @entry_class = QDM::DeviceOrder

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

@@ -3,6 +3,7 @@ module QRDA
     class DiagnosisImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.137']"))
         super(entry_finder)
+        @id_xpath = './cda:entryRelationship/cda:observation/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.135']/cda:value"
         @author_datetime_xpath = "./cda:author/cda:time"
         @prevalence_period_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.135']/cda:effectiveTime"

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

@@ -3,6 +3,7 @@ module QRDA
     class DiagnosticStudyOrderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.17']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @method_xpath = './cda:methodCode'

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

@@ -3,6 +3,7 @@ module QRDA
     class DiagnosticStudyPerformedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.18']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @relevant_period_xpath = "./cda:effectiveTime"
         @author_datetime_xpath = "./cda:author/cda:time"

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

@@ -3,6 +3,7 @@ module QRDA
     class EncounterOrderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.132']"))
         super(entry_finder)
+        @id_xpath = './cda:entryRelationship/cda:encounter/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']/cda:code"
         @author_datetime_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']/cda:author/cda:time"
         @facility_location_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']/cda:participant[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.100']/cda:participantRole[@classCode='SDLOC']/cda:code"

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

@@ -3,6 +3,7 @@ module QRDA
     class EncounterPerformedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.133']"))
         super(entry_finder)
+        @id_xpath = './cda:entryRelationship/cda:encounter/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']/cda:code"
         @relevant_period_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']/cda:effectiveTime"
         @author_datetime_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']/cda:author/cda:time"

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

@@ -3,6 +3,7 @@ module QRDA
     class InterventionOrderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.31']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @entry_class = QDM::InterventionOrder

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

@@ -3,6 +3,7 @@ module QRDA
     class InterventionPerformedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.32']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @relevant_period_xpath = "./cda:effectiveTime"
         @author_datetime_xpath = "./cda:author/cda:time"

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

@@ -3,6 +3,7 @@ module QRDA
     class LaboratoryTestOrderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.37']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @method_xpath = './cda:methodCode'

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

@@ -3,6 +3,7 @@ module QRDA
     class LaboratoryTestPerformedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.38']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @relevant_period_xpath = "./cda:effectiveTime"
         @author_datetime_xpath = "./cda:author/cda:time"

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

@@ -3,6 +3,7 @@ module QRDA
     class PatientCharacteristicExpired < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:value'
         @expired_datetime_xpath = './cda:effectiveTime/cda:low'
         @cause = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.4']/cda:value"

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

@@ -3,6 +3,7 @@ module QRDA
     class PhysicalExamPerformedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.59']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = "./cda:code"
         @relevant_period_xpath = "./cda:effectiveTime"
         @author_datetime_xpath = "./cda:author/cda:time"

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

@@ -3,6 +3,7 @@ module QRDA
     class ProcedureOrderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.63']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @method_xpath = './cda:methodCode'

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

@@ -3,6 +3,7 @@ module QRDA
     class ProcedurePerformedImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']"))
         super(entry_finder)
+        @id_xpath = './cda:id'
         @code_xpath = "./cda:code"
         @relevant_period_xpath = "./cda:effectiveTime"
         @author_datetime_xpath = "./cda:author/cda:time"

data/lib/util/code_system_helper.rb

@@ -34,7 +34,8 @@ module HQMF
         '2.16.840.1.113883.1.11.78' => "HL7 Observation Interpretation",
         '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'
+        '2.16.840.1.113883.18.2' => 'AdministrativeSex',
+        '2.16.840.1.113883.5.1' => 'AdministrativeGender'
       }
 
       CODE_SYSTEM_ALIASES = {

data/lib/util/hqmfr2cql_template_oid_map.json

@@ -219,18 +219,6 @@
       "definition":"care_goal",
       "status":"",
       "negation":false},
-  "2.16.840.1.113883.10.20.28.4.8":{
-      "definition":"communication_from_patient_to_provider",
-      "status":"",
-      "negation":false},
-  "2.16.840.1.113883.10.20.28.4.9":{
-      "definition":"communication_from_provider_to_patient",
-      "status":"",
-      "negation":false},
-  "2.16.840.1.113883.10.20.28.4.10":{
-      "definition":"communication_from_provider_to_provider",
-      "status":"",
-      "negation":false},
   "2.16.840.1.113883.10.20.28.4.13":{
       "definition":"device",
       "status":"applied",
@@ -371,6 +359,10 @@
       "definition":"transfer_to",
       "status":"",
       "negation":false},
+  "2.16.840.1.113883.10.20.28.4.131":{
+    "definition":"assessment",
+    "status":"ordered",
+    "negation":false},
   "2.16.840.1.113883.10.20.28.4.117":{
     "definition":"assessment",
     "status":"performed",
@@ -386,5 +378,13 @@
   "2.16.840.1.113883.10.20.28.4.119": {
     "definition":"allergy_intolerance",
     "status":"",
-    "negation":false}
+    "negation":false},
+  "2.16.840.1.113883.10.20.28.4.130": {
+    "definition":"participation",
+    "status":"",
+    "negation":false},
+  "2.16.840.1.113883.10.20.28.4.132": {
+    "definition":"communication",
+    "status":"performed",
+    "negation":true}
 }

data/lib/util/vsac_api.rb

@@ -0,0 +1,299 @@
+require 'rest_client'
+require 'uri'
+
+module Util
+  module VSAC
+    # Generic VSAC related exception.
+    class VSACError < StandardError
+    end
+
+    # Error represnting a not found response from the API. Includes OID for reporting to user.
+    class VSNotFoundError < VSACError
+      attr_reader :oid
+      def initialize(oid)
+        super("Value Set (#{oid}) was not found.")
+        @oid = oid
+      end
+    end
+
+    # Error represnting a program not found response from the API.
+    class VSACProgramNotFoundError < VSACError
+      attr_reader :oid
+      def initialize(program)
+        super("VSAC Program #{program} does not exist.")
+      end
+    end
+
+    # Error represnting a response from the API that had no concepts.
+    class VSEmptyError < VSACError
+      attr_reader :oid
+      def initialize(oid)
+        super("Value Set (#{oid}) is empty.")
+        @oid = oid
+      end
+    end
+
+    # Raised when the ticket granting ticket has expired.
+    class VSACTicketExpiredError < VSACError
+      def initialize
+        super('VSAC session expired. Please re-enter credentials and try again.')
+      end
+    end
+
+    # Raised when the user credentials were invalid.
+    class VSACInvalidCredentialsError < VSACError
+      def initialize
+        super('VSAC ULMS credentials are invalid.')
+      end
+    end
+
+    # Raised when a call requiring auth is attempted when no ticket_granting_ticket or credentials were provided.
+    class VSACNoCredentialsError < VSACError
+      def initialize
+        super('VSAC ULMS credentials were not provided.')
+      end
+    end
+
+    # Raised when the arguments passed in are bad.
+    class VSACArgumentError < VSACError
+    end
+
+    class VSACAPI
+      # The default program to use for get_program_details and get_program_release_names calls.
+      # This can be overriden by providing a :program in the config or by the single optional parameter for those
+      # methods.
+      DEFAULT_PROGRAM = "CMS eCQM"
+
+      # This is the value of the service parameter passed when getting a ticket. This never changes.
+      TICKET_SERVICE_PARAM = "http://umlsks.nlm.nih.gov"
+
+      # The ticket granting that will be obtained if needed. Accessible so it may be stored in user session.
+      # Is a hash of the :ticket and time it :expires.
+      attr_reader :ticket_granting_ticket
+
+      ##
+      # Creates a new VSACAPI. If credentials were provided they are checked now. If no credentials
+      # are provided then the API can still be used for utility methods.
+      #
+      # Options for the API are passed in as a hash.
+      # * config -
+      def initialize(options)
+        # check that :config exists and has needed fields
+        raise VSACArgumentError.new("Required param :config is missing or empty.") if options[:config].nil?
+        symbolized_config = options[:config].symbolize_keys
+        unless check_config symbolized_config
+          raise VSACArgumentError.new("Required param :config is missing required URLs.")
+        end
+        @config = symbolized_config
+
+        # if a ticket_granting_ticket was passed in, check it and raise errors if found
+        # username and password will be ignored
+        if !options[:ticket_granting_ticket].nil?
+          provided_ticket_granting_ticket = options[:ticket_granting_ticket]
+          if provided_ticket_granting_ticket[:ticket].nil? || provided_ticket_granting_ticket[:expires].nil?
+            raise VSACArgumentError.new("Optional param :ticket_granting_ticket is missing :ticket or :expires")
+          end
+
+          # check if it has expired
+          if Time.now > provided_ticket_granting_ticket[:expires]
+            raise VSACTicketExpiredError.new
+          end
+
+          # ticket granting ticket looks good
+          @ticket_granting_ticket = { ticket: provided_ticket_granting_ticket[:ticket],
+                                      expires: provided_ticket_granting_ticket[:expires] }
+
+        # if username and password were provided use them to get a ticket granting ticket
+        elsif !options[:username].nil? && !options[:password].nil?
+          @ticket_granting_ticket = get_ticket_granting_ticket(options[:username], options[:password])
+        end
+      end
+
+      ##
+      # Gets the list of profiles. This may be used without credentials.
+      #
+      # Returns a list of profile names. These are kept in the order that VSAC provides them in.
+      def get_profile_names
+        profiles_response = RestClient.get("#{@config[:utility_url]}/profiles")
+        profiles = []
+
+        # parse xml response and get text content of each profile element
+        doc = Nokogiri::XML(profiles_response)
+        profile_list = doc.at_xpath("/ProfileList")
+        profile_list.xpath("//profile").each do |profile|
+          profiles << profile.text
+        end
+
+        return profiles
+      end
+
+      ##
+      # Gets the list of programs. This may be used without credentials.
+      #
+      # Returns a list of program names. These are kept in the order that VSAC provides them in.
+      def get_program_names
+        programs_response = RestClient.get("#{@config[:utility_url]}/programs")
+        program_names = []
+
+        # parse json response and return the names of the programs
+        programs_info = JSON.parse(programs_response)['Program']
+        programs_info.each do |program|
+          program_names << program['name']
+        end
+
+        return program_names
+      end
+
+      ##
+      # Gets the details for a program. This may be used without credentials.
+      #
+      # Optional parameter program is the program to request from the API. If it is not provided it will look for
+      # a :program in the config passed in during construction. If there is no :program in the config it will use 
+      # the DEFAULT_PROGRAM constant for the program.
+      #
+      # Returns the JSON parsed response for program details.
+      def get_program_details(program = nil)
+        # if no program was provided use the one in the config or default in constant
+        if program.nil?
+          program = @config.fetch(:program, DEFAULT_PROGRAM)
+        end
+
+        begin
+          # parse json response and return it
+          return JSON.parse(RestClient.get("#{@config[:utility_url]}/program/#{ERB::Util.url_encode(program)}"))
+        rescue RestClient::ResourceNotFound
+          raise VSACProgramNotFoundError.new(program)
+        end
+      end
+
+      ##
+      # Gets the latest profile for a program. This is a separate call from the program details call. It returns JSON
+      # with only the name of the latest profile and the timestamp of the request. ex:
+      #   {
+      #     "name": "eCQM Update 2018-05-04",
+      #     "requestTime": "2018-05-21 03:39:04 PM"
+      #   }
+      #
+      # Optional parameter program is the program to request from the API. If it is not provided it will look for
+      # a :program in the config passed in during construction. If there is no :program in the config it will use 
+      # the DEFAULT_PROGRAM constant for the program.
+      #
+      # Returns the name of the latest profile for the given program.
+      def get_latest_profile_for_program(program = nil)
+        # if no program was provided use the one in the config or default in constant
+        if program.nil?
+          program = @config.fetch(:program, DEFAULT_PROGRAM)
+        end
+
+        begin
+          # parse json response and return it
+          parsed_response = JSON.parse(RestClient.get("#{@config[:utility_url]}/program/#{ERB::Util.url_encode(program)}/latest%20profile"))
+
+          # As of 5/17/18 VSAC does not return 404 when an invalid profile is provided. It just doesnt fill the name
+          # attribute in the 200 response. We need to check this.
+          raise VSACProgramNotFoundError.new(program) if parsed_response['name'].nil?
+          return parsed_response['name']
+
+        # keeping this rescue block in case the API is changed to return 404 for invalid profile
+        rescue RestClient::ResourceNotFound
+          raise VSACProgramNotFoundError.new(program)
+        end
+      end
+
+      ##
+      # Gets the releases for a program. This may be used without credentials.
+      #
+      # Optional parameter program is the program to request from the API. If it is not provided it will look for
+      # a :program in the config passed in during construction. If there is no :program in the config it will use
+      # the DEFAULT_PROGRAM constant for the program.
+      #
+      # Returns a list of release names in a program. These are kept in the order that VSAC provides them in.
+      def get_program_release_names(program = nil)
+        program_details = get_program_details(program)
+        releases = []
+
+        # pull just the release names out
+        program_details['release'].each do |release|
+          releases << release['name']
+        end
+
+        return releases
+      end
+
+      ##
+      # Gets a valueset. This requires credentials.
+      #
+      def get_valueset(oid, options = {})
+        # base parameter oid is always needed
+        params = { id: oid }
+
+        # release parameter, should be used moving forward
+        unless options[:release].nil?
+          params[:release] = options[:release]
+        end
+
+        # profile parameter, may be needed for getting draft value sets
+        if !options[:profile].nil?
+          params[:profile] = options[:profile]
+          unless options[:include_draft].nil?
+            params[:includeDraft] = !options[:include_draft].nil? ? 'yes' : 'no'
+          end
+        else
+          unless options[:include_draft].nil?
+            raise VSACArgumentError.new("Option :include_draft requires :profile to be provided.")
+          end
+        end
+
+        # version parameter, rarely used
+        unless options[:version].nil?
+          params[:version] = options[:version]
+        end
+
+        # get a new service ticket
+        params[:ticket] = get_ticket
+
+        # run request
+        begin
+          return RestClient.get("#{@config[:content_url]}/RetrieveMultipleValueSets", params: params)
+        rescue RestClient::ResourceNotFound
+          raise VSNotFoundError.new(oid)
+        rescue RestClient::InternalServerError
+          raise VSACError.new("Server error response from VSAC for (#{oid}).")
+        end
+      end
+
+      private
+
+      def get_ticket
+        # if there is no ticket granting ticket then we should raise an error
+        raise VSACNoCredentialsError.new unless @ticket_granting_ticket
+        # if the ticket granting ticket has expired, throw an error
+        raise VSACTicketExpiredError.new if Time.now > @ticket_granting_ticket[:expires]
+
+        # attempt to get a ticket
+        begin
+          ticket = RestClient.post("#{@config[:auth_url]}/Ticket/#{@ticket_granting_ticket[:ticket]}", service: TICKET_SERVICE_PARAM)
+          return ticket.to_s
+        rescue RestClient::Unauthorized
+          @ticket_granting_ticket[:expires] = Time.now
+          raise VSACTicketExpiredError.new
+        end
+      end
+
+      def get_ticket_granting_ticket(username, password)
+        ticket = RestClient.post("#{@config[:auth_url]}/Ticket", username: username, password: password)
+        return { ticket: String.new(ticket), expires: Time.now + 8.hours }
+      rescue RestClient::Unauthorized
+        raise VSACInvalidCredentialsError.new
+      end
+
+      # Checks to ensure the API config has all necessary fields
+      def check_config(config)
+        return !config.nil? &&
+               !config[:auth_url].nil? &&
+               !config[:content_url].nil? &&
+               !config[:utility_url].nil?
+      end
+    end
+  end
+end

metadata

@@ -1,15 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: cqm-parsers
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-10-09 00:00:00.000000000 Z
+date: 2019-01-25 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: mustache
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
@@ -376,6 +390,7 @@ files:
 - lib/util/hqmf_template_oid_map.json
 - lib/util/hqmfr2_template_oid_map.json
 - lib/util/hqmfr2cql_template_oid_map.json
+- lib/util/vsac_api.rb
 homepage: https://github.com/projecttacoma/cqm-parsers
 licenses:
 - Apache-2.0
@@ -396,7 +411,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 2.7.7
 signing_key: 
 specification_version: 4
 summary: A library for parsing HQMF documents.