cqm-converter 0.3.4 → 0.3.6

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 8553e2f135b2682dda45008155b9656f9bba5ee7
+  metadata.gz: 877c904445ba40b62519fdcddb7509a4e440c2d1
+  data.tar.gz: ac4b3fda4196682999230c07ff66b02b9144ba0b
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+  data.tar.gz: b2ca77ebd8a042ad05c733414c7588fe0f2ae64877e9bc272d96c8f03355ebd69de80110f7358520a20765fe6316cddd559dc0a0b49eb0465bf26e574cb82f91

data/.rubocop.yml

@@ -12,6 +12,8 @@ Metrics/LineLength:
 
 Metrics/BlockLength:
   Max: 50
+  Exclude:
+    - 'spec/**/*_spec.rb'
 
 Metrics/AbcSize:
   Max: 130
@@ -38,4 +40,8 @@ Metrics/MethodLength:
   Max: 60
 
 Style/IfUnlessModifier:
-  Enabled: false
+  Enabled: false
+
+Lint/UnusedMethodArgument:
+  Exclude:
+    - 'lib/ext/mongoid.rb'

data/Gemfile

@@ -2,6 +2,8 @@ source 'https://rubygems.org'
 
 git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
 
-gem 'cql_qdm_patientapi', github: 'projecttacoma/cql_qdm_patientapi', branch: 'adam_taco'
+gem 'cql_qdm_patientapi', github: 'projecttacoma/cql_qdm_patientapi', branch: 'master'
+
+# gem 'cqm-models', github: 'projecttacoma/cqm-models', branch: 'master'
 
 gemspec

data/cqm-converter.gemspec

@@ -3,7 +3,7 @@ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 
 Gem::Specification.new do |spec|
   spec.name          = 'cqm-converter'
-  spec.version       = '0.3.4'
+  spec.version       = '0.3.6'
   spec.authors       = ['aholmes@mitre.org']
   spec.email         = ['aholmes@mitre.org']
 
@@ -22,9 +22,9 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'bundler'
   spec.add_development_dependency 'byebug'
   spec.add_runtime_dependency 'coffee-script'
-  spec.add_runtime_dependency 'cqm-models', '>= 0.7.2'
+  spec.add_runtime_dependency 'cqm-models', '>= 0.8.4'
   spec.add_runtime_dependency 'execjs'
-  spec.add_runtime_dependency 'health-data-standards', '>= 4.0.3'
+  spec.add_runtime_dependency 'health-data-standards', '>= 4.1.0'
   spec.add_runtime_dependency 'momentjs-rails'
   spec.add_development_dependency 'rake'
   spec.add_development_dependency 'rspec'

data/lib/cqm/converter.rb

@@ -9,6 +9,7 @@ module CQM
   end
 end
 
+require_relative '../ext/mongoid'
 require_relative 'converter/utils'
 require_relative 'converter/hds_record'
 require_relative 'converter/qdm_patient'

data/lib/cqm/converter/hds_record.rb

@@ -72,7 +72,11 @@ module CQM::Converter
       ethnicity = record.ethnicity
       if ethnicity
         # See: https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.6.238
-        code = QDM::Code.new(ethnicity['code'], 'cdcrec', ethnicity['name'], '2.16.840.1.113883.6.238')
+        # Bonnie currently uses 'CDC Race' instead of the correct 'cdcrec'.  This incorrect code is here as a temporary
+        # workaround until the larger change of making bonnie use 'cdcrec' can be implemented.
+        # Same change is present in `race` below.
+        code = QDM::Code.new(ethnicity['code'], 'CDC Race', ethnicity['name'], '2.16.840.1.113883.6.238')
+        # code = QDM::Code.new(ethnicity['code'], 'cdcrec', ethnicity['name'], '2.16.840.1.113883.6.238')
         patient.dataElements << QDM::PatientCharacteristicEthnicity.new(dataElementCodes: [code])
       end
 
@@ -88,7 +92,8 @@ module CQM::Converter
       race = record.race
       if race
         # See: https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.6.238
-        code = QDM::Code.new(race['code'], 'cdcrec', race['name'], '2.16.840.1.113883.6.238')
+        code = QDM::Code.new(race['code'], 'CDC Race', race['name'], '2.16.840.1.113883.6.238')
+        # code = QDM::Code.new(race['code'], 'cdcrec', race['name'], '2.16.840.1.113883.6.238')
         patient.dataElements << QDM::PatientCharacteristicRace.new(dataElementCodes: [code])
       end
 
@@ -127,11 +132,11 @@ module CQM::Converter
     end
 
     def generate_qdm_data_element(dc_fixed_keys, dc_type)
-      data_element = QDM.const_get(dc_type).new.from_json(dc_fixed_keys.to_json)
+      data_element = QDM.const_get(dc_type).new(dc_fixed_keys)
 
       # Any nested QDM types that need initialization should be handled here
       # when converting from the QDM models to the HDS models.
-      # For now, that should just be FacilityLocation objects
+      # For now, that should just be FacilityLocation objects and Id
       if data_element.is_a?(QDM::EncounterPerformed)
         data_element.facilityLocations = data_element.facilityLocations.map do |facility|
           QDM::FacilityLocation.new.from_json(facility.to_json)

data/lib/cqm/converter/utils.rb

@@ -34,6 +34,9 @@ module CQM::Converter
         if QDM.const_get(model).respond_to?('fields')
           qdm_model_attrs[model.to_s] = QDM.const_get(model).fields.keys.map! { |a| a.camelize(:lower) }
         end
+        if QDM.const_get(model).respond_to?('embedded_relations')
+          qdm_model_attrs[model.to_s].concat(QDM.const_get(model).embedded_relations.keys.map! { |a| a.camelize(:lower) })
+        end
       end
       # TODO: These fields are currently not supported. See:
       # https://github.com/projecttacoma/cql_qdm_patientapi/search?q=does+not+currently+support
@@ -135,6 +138,7 @@ module CQM::Converter
             results['description'] = datatype['entry']['description'];
             // Add oid to result.
             results['hqmfOid'] = datatype['entry']['oid'];
+
             processed_datatypes[key].push(results);
           });
         });

data/lib/ext/mongoid.rb

@@ -0,0 +1,12 @@
+module BSON
+  # Monkey patch BSON::ObjectId to just return the string for to_json. This is done to match operation in bonnie.
+  class ObjectId
+    def to_json(*args)
+      to_s.to_json
+    end
+
+    def as_json(*args)
+      to_s.as_json
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-converter
 version: !ruby/object:Gem::Version
-  version: 0.3.4
+  version: 0.3.6
 platform: ruby
 authors:
 - aholmes@mitre.org
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2018-06-22 00:00:00.000000000 Z
+date: 2018-08-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -72,14 +72,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.7.2
+        version: 0.8.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.7.2
+        version: 0.8.4
 - !ruby/object:Gem::Dependency
   name: execjs
   requirement: !ruby/object:Gem::Requirement
@@ -100,14 +100,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.3
+        version: 4.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.3
+        version: 4.1.0
 - !ruby/object:Gem::Dependency
   name: momentjs-rails
   requirement: !ruby/object:Gem::Requirement
@@ -201,6 +201,7 @@ files:
 - lib/cqm/converter/hds_record.rb
 - lib/cqm/converter/qdm_patient.rb
 - lib/cqm/converter/utils.rb
+- lib/ext/mongoid.rb
 - lib/tasks/hds.rake
 - lib/tasks/qdm.rake
 homepage: https://github.com/projecttacoma/cqm-converter
@@ -223,7 +224,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.11
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: HDS <=> QDM Model Converter