cqm-parsers 2.0.1 → 3.0.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 18055a1d7aaebcaeee25ae76ad02b7a0bbdc4022
+  metadata.gz: 9946e3dc5e1e74875ed24bb690332fc260f0b103
+  data.tar.gz: aa9298b5a7e4790a0534210a1278ec3b78ad387c
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data/Gemfile

@@ -2,9 +2,9 @@ source 'https://rubygems.org'
 
 gemspec :development_group => :test
 
-gem 'mongoid', '~> 6.4.2'
+gem 'mongoid', '~> 5.0.0'
 
-gem 'cqm-models', '~> 2.0.0'
+# gem 'cqm-models', '~> 3.0.0'
 # gem 'cqm-models', git: 'https://github.com/projecttacoma/cqm-models.git', branch: 'master'
 # gem 'cqm-models', :path => '../cqm-models'
 

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

@@ -74,7 +74,7 @@ module HQMF2
       fail 'Measure Observations criteria is missing computed expression(s) ' if exp.nil?
       parts = exp.to_s.split('-')
       dc = parse_parts_to_dc(parts)
-      @doc.add_data_criteria(dc)
+      @doc.add_data_criteria(dc) unless dc.nil?
       # Update reference_ids with any newly referenced data criteria
       dc.children_criteria.each { |cc| @doc.add_reference_id(cc) } unless dc&.children_criteria.nil?
       dc

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

@@ -11,7 +11,7 @@ module HQMF2CQL
     end
 
     # Extracts potential measure observations from the CQL based HQMF.
-    # This function needs to return a boolean so that it will continue to work with 
+    # This function needs to return a boolean so that it will continue to work with
     # HQMF2::DocumentPopulationHelper::extract_populations_and_criteria
     # This function is being overridden because in CQL the observations are no longer data criteria in the HQMF.
     def extract_observations
@@ -22,10 +22,10 @@ module HQMF2CQL
       observation_section = @doc.xpath('/cda:QualityMeasureDocument/cda:component/cda:measureObservationSection',
                                        HQMF2::Document::NAMESPACES)
       unless observation_section.empty?
-        observation_section.each do |entry|
+        observation_section.xpath('cda:definition').each do |obs_def|
           # Need to add population criteria for observations
           criteria_id = 'OBSERV'
-          criteria = HQMF2::PopulationCriteria.new(entry.xpath('cda:definition'), @document, @id_generator)
+          criteria = HQMF2::PopulationCriteria.new(obs_def, @document, @id_generator)
           criteria.type = 'OBSERV'
           if @ids_by_hqmf_id["#{criteria.hqmf_id}"]
             criteria.create_human_readable_id(@ids_by_hqmf_id[criteria.hqmf_id])
@@ -39,16 +39,16 @@ module HQMF2CQL
           cql_define_function = {}
           # 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[:function_aggregation_type] = entry.at_xpath("*/cda:measureObservationDefinition/cda:methodCode/cda:item").attributes['code'].value
-          cql_define_function[:function_hqmf_oid] = entry.at_xpath("*/cda:measureObservationDefinition/cda:id").attributes['root'].value
+          cql_define_function[:function_name] = obs_def.at_xpath("cda:measureObservationDefinition/cda:value/cda:expression").values.first.match('\\"([A-Za-z0-9 ]+)\\"')[1]
+          cql_define_function[:function_aggregation_type] = obs_def.at_xpath("cda:measureObservationDefinition/cda:methodCode/cda:item").attributes['code'].value
+          cql_define_function[:function_hqmf_oid] = obs_def.at_xpath("cda:measureObservationDefinition/cda:id").attributes['root'].value
           # 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
+          measure_population_id = obs_def.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
 
-          measure_population_name = entry.at_xpath("*/cda:measureObservationDefinition/cda:component/cda:criteriaReference/cda:id").attributes['extension'].value
-          # Get the name of the parameter to the observation function within the relevant population criteria section
-          cql_define_function[:parameter] = @doc.at_xpath("cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection/cda:component/cda:#{measure_population_name}Criteria/cda:id[@root = \"#{measure_population_id}\"]/../cda:precondition/cda:criteriaReference/cda:id").attributes['extension'].value.match('\\"([A-Za-z0-9 ]+)\\"')[1]
+          measure_population_name = obs_def.at_xpath("cda:measureObservationDefinition/cda:component/cda:criteriaReference/cda:id").attributes['extension'].value
+          criteria_reference_id = @doc.at_xpath("cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection/cda:component/cda:#{measure_population_name}Criteria/cda:id[@root = \"#{measure_population_id}\"]/../cda:precondition/cda:criteriaReference/cda:id")
+          cql_define_function[:parameter] = criteria_reference_id.attributes['extension'].value.match('\\"([A-Za-z0-9 ]+)\\"')[1]
 
           @observations << cql_define_function
         end

data/lib/measure-loader/mat_measure_files.rb

@@ -53,7 +53,7 @@ module Measures
 
       def unzip_measure_zip_into_hash(zip_file)
         folders = Hash.new { |h, k| h[k] = {files: []} }
-        Zip::File.open zip_file do |file|
+        Zip::File.open zip_file.path do |file|
           file.each do |f|
             pn = Pathname(f.name)
             next if '__MACOSX'.in? pn.each_filename  # ignore anything in a __MACOSX folder

data/lib/measure-loader/source_data_criteria_loader.rb

@@ -26,7 +26,9 @@ module Measures
                         extract_fields_from_single_code_reference_data_criteria(criteria)
                       end
       hqmf_template_oid = criteria.at_css('templateId/item')['root']
-      model = QDM::ModelFinder.by_hqmf_oid(hqmf_template_oid).new(model_fields)
+      model = QDM::ModelFinder.by_hqmf_oid(hqmf_template_oid)
+      raise "No datatype found for oid #{hqmf_template_oid}. Verify the QDM version of the measure package is correct." if model.nil?
+      model = model.new(model_fields)
       model.description = model.qdmTitle + ': ' + model.description
       return model
     end
@@ -42,9 +44,9 @@ module Measures
     end
 
     def extract_fields_from_single_code_reference_data_criteria(criteria)
-      single_code_reference = criteria.css('value[codeSystem][code]').last || criteria.css('code[codeSystem][code]').last
+      single_code_reference = criteria.at_css('value[codeSystem][code]') || criteria.at_css('code[codeSystem][code]')
       system_id = "#{single_code_reference['codeSystem']}_#{single_code_reference['codeSystemVersion']}".to_sym
-      concept = @single_code_concepts[system_id][single_code_reference['code'].to_sym]
+      concept = @single_code_concepts[system_id][single_code_reference['code'].to_sym] || get_concept_from_participation(criteria.at_css('participation'))
       value_set = concept._parent
       return {
         description: concept.display_name,
@@ -52,6 +54,14 @@ module Measures
       }
     end
 
+    # If QDM datatype template in MAT has includeSubTemplate, code gets nested into participation
+    # this method gets the codes from participation and form the code concept
+    def get_concept_from_participation(participation)
+      code_element = participation.at_css('code')
+      system_id = "#{code_element['codeSystem']}_#{code_element['codeSystemVersion']}".to_sym
+      @single_code_concepts[system_id][code_element['code'].to_sym]
+    end
+
     def map_single_code_concepts(value_sets_from_single_code_references)
       single_code_concepts = {}
       value_sets_from_single_code_references.flat_map(&:concepts).each do |concept|

data/lib/tasks/hqmf.rake

@@ -1,7 +1,7 @@
 require 'pathname'
 require 'fileutils'
 require 'json'
-require 'hqmf-parser'
+require 'cqm-parsers'
 
 namespace :hqmf do
 

data/lib/util/vsac_api.rb

@@ -138,7 +138,7 @@ module Util
       # 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 
+      # 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.
@@ -159,7 +159,7 @@ module Util
       #   }
       #
       # 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 
+      # 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.
@@ -242,8 +242,8 @@ module Util
       def get_multiple_valueset_raw_responses(needed_value_sets)
         service_tickets = get_service_tickets(needed_value_sets.size)
 
-        hydra = Typhoeus::Hydra.new # Hydra executes multiple HTTP requests at once
-        requests = needed_value_sets.map do |n| 
+        hydra = Typhoeus::Hydra.new(max_concurrency: 1) # Hydra executes multiple HTTP requests at once
+        requests = needed_value_sets.map do |n|
           request = create_valueset_request(n[:value_set][:oid], service_tickets.pop, n[:vs_vsac_options])
           hydra.queue(request)
           request
@@ -258,7 +258,7 @@ module Util
       def get_service_tickets(amount)
         raise VSACNoCredentialsError.new unless @ticket_granting_ticket
         raise VSACTicketExpiredError.new if Time.now > @ticket_granting_ticket[:expires]
-        
+
         hydra = Typhoeus::Hydra.new # Hydra executes multiple HTTP requests at once
         requests = amount.times.map do
           request = create_service_ticket_request
@@ -299,7 +299,7 @@ module Util
 
       # Create a typheous request for a service ticket (this must be executed later)
       def create_service_ticket_request
-        return Typhoeus::Request.new("#{@config[:auth_url]}/Ticket/#{@ticket_granting_ticket[:ticket]}", 
+        return Typhoeus::Request.new("#{@config[:auth_url]}/Ticket/#{@ticket_granting_ticket[:ticket]}",
                                      method: :post,
                                      params: { service: TICKET_SERVICE_PARAM})
       end
@@ -307,7 +307,7 @@ module Util
       # Use your username and password to retrive a ticket granting ticket from VSAC
       def get_ticket_granting_ticket(username, password)
         response = Typhoeus.post(
-          "#{@config[:auth_url]}/Ticket", 
+          "#{@config[:auth_url]}/Ticket",
           # looks like typheous sometimes switches the order of username/password when encoding
           # which vsac cant handle (!?), so encode first
           body: URI.encode_www_form(username: username, password: password)

metadata

@@ -1,15 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: cqm-parsers
 version: !ruby/object:Gem::Version
-  version: 2.0.1
+  version: 3.0.0.0
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-10-01 00:00:00.000000000 Z
+date: 2020-06-30 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: cqm-models
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.0
 - !ruby/object:Gem::Dependency
   name: mustache
   requirement: !ruby/object:Gem::Requirement
@@ -30,84 +44,84 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.7'
+        version: 2.7.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.7'
+        version: 2.7.0
 - !ruby/object:Gem::Dependency
   name: mongoid
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '6.4'
+        version: 5.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '6.4'
+        version: 5.0.0
 - !ruby/object:Gem::Dependency
   name: mongoid-tree
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: 2.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5.0'
+        version: 4.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5.0'
+        version: 4.2.0
 - !ruby/object:Gem::Dependency
-  name: protected_attributes_continued
+  name: protected_attributes
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: 1.0.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: 1.0.5
 - !ruby/object:Gem::Dependency
   name: uuid
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.3'
+        version: 2.3.7
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.3'
+        version: 2.3.7
 - !ruby/object:Gem::Dependency
   name: builder
   requirement: !ruby/object:Gem::Requirement
@@ -126,58 +140,64 @@ dependencies:
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.8.5
+    - - "<"
       - !ruby/object:Gem::Version
-        version: '1.10'
+        version: 1.11.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.10'
+        version: 1.8.5
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: 1.11.0
 - !ruby/object:Gem::Dependency
   name: highline
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: 1.7.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: 1.7.0
 - !ruby/object:Gem::Dependency
   name: rubyzip
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: '1.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: '1.3'
 - !ruby/object:Gem::Dependency
   name: typhoeus
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: zip-zip
   requirement: !ruby/object:Gem::Requirement
@@ -198,28 +218,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.1'
+        version: 1.1.10
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.1'
+        version: 1.1.10
 - !ruby/object:Gem::Dependency
   name: memoist
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: 0.9.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: 0.9.1
 description: A library for parsing HQMF documents.
 email: tacoma-list@lists.mitre.org
 executables: []
@@ -229,6 +249,7 @@ files:
 - Gemfile
 - README.md
 - Rakefile
+- lib/cqm-parsers.rb
 - lib/ext/data_element.rb
 - lib/hqmf-model/attribute.rb
 - lib/hqmf-model/data_criteria.json
@@ -238,7 +259,6 @@ files:
 - lib/hqmf-model/precondition.rb
 - lib/hqmf-model/types.rb
 - lib/hqmf-model/utilities.rb
-- lib/hqmf-parser.rb
 - lib/hqmf-parser/1.0/attribute.rb
 - lib/hqmf-parser/1.0/comparison.rb
 - lib/hqmf-parser/1.0/data_criteria.rb