cqm-parsers 3.2.0.2 → 4.0.0.0

checksums.yaml

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

@@ -2,9 +2,8 @@ source 'https://rubygems.org'
 
 gemspec :development_group => :test
 
-gem 'mongoid', '~> 7.0.5'
+gem 'mongoid', '~> 6.4.2'
 
-# 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/README.md

@@ -42,22 +42,9 @@ bundle exec rake test
 
 ```
 
-
 ## Versioning
 
-Starting with version **2.0.0** released on 6/20/19, cqm-parsers versioning has the format **X.Y.Z**, where:
-
-* **X** maps to a version of the CQL-based HQMF IG. See the table below to see the existing mapping to CQL-based HQMF IG versions.
-
-  | X | CQL-based HQMF IG|
-  | --- | --- |
-  | 2 | R1 STU3 |
-
-* **Y** indicates major changes (incompatible API changes)
-
-* **Z** indicates minor changes (added functionality in a backwards-compatible manner) and patch changes (backwards-compatible bug fixes)
-
-For the versions available, see [tags on this repository](https://github.com/projecttacoma/cqm-parsers/tags).
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see [tags on this repository](https://github.com/projecttacoma/cqm-parsers/tags). 
 
 ## License
 

data/lib/measure-loader/mat_measure_files.rb

@@ -58,7 +58,7 @@ module Measures
             pn = Pathname(f.name)
             next if '__MACOSX'.in? pn.each_filename  # ignore anything in a __MACOSX folder
             next unless pn.basename.extname.in? ['.xml','.cql','.json','.html']
-            folders[pn.dirname][:files] << { basename: pn.basename, contents: f.get_input_stream.read }
+            folders[pn.dirname][:files] << { basename: pn.basename, contents: f.get_input_stream.read.force_encoding('UTF-8') }
             folders[pn.dirname][:depth] =  pn.each_filename.count # this is just a count of how many folders are in the path
           end
         end
@@ -135,4 +135,4 @@ module Measures
 
     end
   end
-end
+end

data/lib/measure-loader/source_data_criteria_loader.rb

@@ -46,7 +46,8 @@ module Measures
     def extract_fields_from_single_code_reference_data_criteria(criteria)
       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] || get_concept_from_participation(criteria.at_css('participation'))
+      # concept = @single_code_concepts[system_id]&[single_code_reference['code'].to_sym] || get_concept_from_participation(criteria.at_css('participation'))
+      concept = @single_code_concepts&.dig(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,

data/lib/measure-loader/vsac_value_set_loader.rb

@@ -7,8 +7,7 @@ module Measures
       options.symbolize_keys!
       @vsac_options = options[:options]
       @vsac_ticket_granting_ticket = options[:ticket_granting_ticket]
-      @vsac_username = options[:username]
-      @vsac_password = options[:password]
+      @vsac_api_key = options[:api_key]
       @vs_model_cache = {}
     end
 
@@ -48,7 +47,7 @@ module Measures
 
     def load_api
       return @api if @api.present?
-      @api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], ticket_granting_ticket: @vsac_ticket_granting_ticket, username: @vsac_username, password: @vsac_password)
+      @api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], ticket_granting_ticket: @vsac_ticket_granting_ticket, api_key: @vsac_api_key)
       return @api
     end
 

data/lib/util/hqmfr2cql_template_oid_map.json

@@ -219,10 +219,6 @@
       "definition":"care_goal",
       "status":"",
       "negation":false},
-  "2.16.840.1.113883.10.20.28.4.13":{
-      "definition":"device",
-      "status":"applied",
-      "negation":false},
   "2.16.840.1.113883.10.20.28.4.11":{
       "definition":"device_adverse_event",
       "status":"",

data/lib/util/vsac_api.rb

@@ -7,7 +7,7 @@ module Util
     class VSACError < StandardError
     end
 
-    # Error represnting a not found response from the API. Includes OID for reporting to user.
+    # Error representing a not found response from the API. Includes OID for reporting to user.
     class VSNotFoundError < VSACError
       attr_reader :oid
       def initialize(oid)
@@ -23,7 +23,7 @@ module Util
       end
     end
 
-    # Error represnting a program not found response from the API.
+    # Error representing a program not found response from the API.
     class VSACProgramNotFoundError < VSACError
       attr_reader :oid
       def initialize(program)
@@ -31,7 +31,7 @@ module Util
       end
     end
 
-    # Error represnting a response from the API that had no concepts.
+    # Error representing a response from the API that had no concepts.
     class VSEmptyError < VSACError
       attr_reader :oid
       def initialize(oid)
@@ -50,14 +50,14 @@ module Util
     # Raised when the user credentials were invalid.
     class VSACInvalidCredentialsError < VSACError
       def initialize
-        super('VSAC ULMS credentials are invalid.')
+        super('VSAC UMLS 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.')
+        super('VSAC UMLS credentials were not provided.')
       end
     end
 
@@ -93,7 +93,7 @@ module Util
         end
 
         # if a ticket_granting_ticket was passed in, check it and raise errors if found
-        # username and password will be ignored
+        # VSAC API Key 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?
@@ -105,9 +105,9 @@ module Util
           @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])
+          # if api key was provided use it to get a ticket granting ticket
+        elsif !options[:api_key].nil?
+          @ticket_granting_ticket = get_ticket_granting_ticket(options[:api_key])
         end
       end
 
@@ -304,13 +304,11 @@ module Util
                                      params: { service: TICKET_SERVICE_PARAM})
       end
 
-      # Use your username and password to retrive a ticket granting ticket from VSAC
-      def get_ticket_granting_ticket(username, password)
+      # Use your API Key to retrive a ticket granting ticket from VSAC
+      def get_ticket_granting_ticket(api_key)
         response = Typhoeus.post(
           "#{@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)
+          body: URI.encode_www_form(apikey: api_key)
         )
         raise VSACInvalidCredentialsError.new if response.response_code == 401
         validate_http_status(response.response_code)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-parsers
 version: !ruby/object:Gem::Version
-  version: 3.2.0.2
+  version: 4.0.0.0
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-02-28 00:00:00.000000000 Z
+date: 2021-10-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: 4.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: 4.0.0
 - !ruby/object:Gem::Dependency
   name: mustache
   requirement: !ruby/object:Gem::Requirement
@@ -58,56 +58,42 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 7.0.5
+        version: 6.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 7.0.5
+        version: 6.4.2
 - !ruby/object:Gem::Dependency
   name: mongoid-tree
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: 2.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: 2.1.0
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '6.0'
+        version: 5.2.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '6.0'
-- !ruby/object:Gem::Dependency
-  name: protected_attributes_continued
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 1.4.0
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 1.4.0
+        version: 5.2.1
 - !ruby/object:Gem::Dependency
   name: uuid
   requirement: !ruby/object:Gem::Requirement
@@ -145,7 +131,7 @@ dependencies:
         version: 1.8.5
     - - "<"
       - !ruby/object:Gem::Version
-        version: 1.14.0
+        version: 1.13.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -155,7 +141,7 @@ dependencies:
         version: 1.8.5
     - - "<"
       - !ruby/object:Gem::Version
-        version: 1.14.0
+        version: 1.13.0
 - !ruby/object:Gem::Dependency
   name: highline
   requirement: !ruby/object:Gem::Requirement
@@ -343,7 +329,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.3
+rubygems_version: 3.0.2
 signing_key:
 specification_version: 4
 summary: A library for parsing HQMF documents.