cqm-models 4.1.1 → 4.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 3b776247323332ba61b8df7b85393f9cc69e8388d15dc3d55a4d7bfcfd3d2be2
+  data.tar.gz: 57d99f0316933ab3886aa50e25a65c791d0996ff8b7d9cd38766f056b22a9793
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+  data.tar.gz: f4c50758a5342921502da3389e2410c05d1a0004e6f9072cf9216cbb5b987ad3960353dbc896b9b6dece71903e897000a59f29ac8c0ce1c8273a918a16da0e58

data/.github/workflows/ci.yml

@@ -12,21 +12,21 @@ jobs:
 
     strategy:
       matrix:
-        ruby-version: [2.6, 2.7]
-        mongodb-version: [4.0.18, 4.4]
-        node-version: [12.x, 14.x]
+        ruby-version: [3.0]
+        mongodb-version: [4.2, 4.4]
+        node-version: [18.x]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Use Ruby ${{ matrix.ruby-version }}
       uses: ruby/setup-ruby@v1
       with:
         ruby-version: ${{ matrix.ruby-version }}
-        bundler: 2.1.4
+        bundler: 2.3.17
     - name: Install dependencies
       run: bundle install
     - name: Start MongoDB
-      uses: supercharge/mongodb-github-action@1.3.0
+      uses: supercharge/mongodb-github-action@1.10.0
       with:
         mongodb-version: ${{ matrix.mongodb-version }}
     - name: Run audit
@@ -38,7 +38,7 @@ jobs:
     - name: Run rubocop
       run: bundle exec rubocop
     - name: Use Node.js ${{ matrix.node-version }}
-      uses: actions/setup-node@v2
+      uses: actions/setup-node@v3
       with:
         node-version: ${{ matrix.node-version }}
     - name: Install Yarn
@@ -53,4 +53,3 @@ jobs:
       run: |
         ./bin/validate_dist.sh
         ./bin/validate_browser.sh
-        ./bin/validate_generator.sh

data/app/assets/javascripts/QDMPatient.js

@@ -3,6 +3,7 @@ const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+const AnyEntity = require('./basetypes/AnyEntity');
 const AllDataElements = require('./AllDataElements');
 
 const [Schema, Number, String, Mixed] = [
@@ -94,6 +95,12 @@ QDMPatientSchema.methods.getDataElements = function getDataElements(params) {
   return this.dataElements;
 };
 
+QDMPatientSchema.methods.addMethodsTo = function addMethodsTo(obj, methods) {
+  Object.entries(methods).forEach(([method_name, method]) => {
+    obj[method_name] = method;
+  });
+};
+
 // Returns an array of dataElements that exist on the patient, queried by
 // QDM profile
 // @param {string} profile - the data criteria requested by the execution engine
@@ -105,10 +112,26 @@ QDMPatientSchema.methods.getByProfile = function getByProfile(profile, isNegated
   // If isNegated == null, return all matching data elements by type, regardless of negationRationale.
   const results = this.dataElements.filter(element => (element._type === `QDM::${profile}` || element._type === profile) && (isNegated === null || !!element.negationRationale === isNegated));
   return results.map((result) => {
+    // we need to convert mongoose document to an object.
+    // This is required for comparing the two objects(in cql-execution) as we can't compare two mongoose documents.
     const removedMongooseItems = new AllDataElements[profile](result).toObject({ virtuals: true });
     // toObject() will remove all mongoose functions but also remove the schema methods, so we add them back
-    Object.entries(result.schema.methods).forEach(([method_name, method]) => {
-      removedMongooseItems[method_name] = method;
+    this.addMethodsTo(removedMongooseItems, result.schema.methods);
+    // add methods to entities
+    Object.entries(result).forEach(([key, values]) => {
+      // entities are always an array
+      if (Array.isArray(values)) {
+        try {
+          // check if the attribute is of Entity
+          if (AnyEntity.prototype.cast(values[0])) {
+            values.forEach((value, index) => {
+              const entity = removedMongooseItems[key][index];
+              this.addMethodsTo(entity, value.schema.methods);
+            });
+          }
+          // eslint-disable-next-line no-empty
+        } catch (e) {}
+      }
     });
     return removedMongooseItems;
   });

data/app/assets/javascripts/attributes/Component.js

@@ -44,6 +44,23 @@ function ComponentSchemaFunction(add, options) {
     extended.add(add);
   }
 
+  /* eslint no-underscore-dangle: 0 */
+  extended.methods._is = function _is(typeSpecifier) {
+    return this._typeHierarchy().some(
+      t => t.type === typeSpecifier.type && t.name === typeSpecifier.name
+    );
+  };
+
+  extended.methods._typeHierarchy = function _typeHierarchy() {
+    const typeName = this._type.replace(/QDM::/, '');
+    const ver = this.qdmVersion.replace('.', '_');
+    return [
+      {
+        name: `{urn:healthit-gov:qdm:v${ver}}${typeName}`,
+        type: 'NamedTypeSpecifier',
+      },
+    ];
+  };
   return extended;
 }
 

data/app/assets/javascripts/attributes/Entity.js

@@ -51,6 +51,23 @@ function EntitySchemaFunction(add, options) {
     extended.add(add);
   }
 
+  /* eslint no-underscore-dangle: 0 */
+  extended.methods._is = function _is(typeSpecifier) {
+    return this._typeHierarchy().some(
+      t => t.type === typeSpecifier.type && t.name === typeSpecifier.name
+    );
+  };
+
+  extended.methods._typeHierarchy = function _typeHierarchy() {
+    const typeName = this._type.replace(/QDM::/, '');
+    const ver = this.qdmVersion.replace('.', '_');
+    return [
+      {
+        name: `{urn:healthit-gov:qdm:v${ver}}${typeName}`,
+        type: 'NamedTypeSpecifier',
+      },
+    ];
+  };
   return extended;
 }
 

data/app/assets/javascripts/basetypes/AnyEntity.js

@@ -15,7 +15,7 @@ AnyEntity.prototype.cast = (entity) => {
     return null;
   }
 
-  if (entity instanceof PatientEntity || entity instanceof Practitioner || entity instanceof CarePartner || entity instanceof Organization) {
+  if (entity instanceof PatientEntity || entity instanceof Practitioner || entity instanceof CarePartner || entity instanceof Organization || entity instanceof Location) {
     return entity;
   }
 

data/app/models/cqm/individual_result.rb

@@ -35,8 +35,8 @@ module CQM
     field :state, type: String, default: 'queued'
 
     # Relations to other model classes
-    belongs_to :measure
-    belongs_to :patient
+    belongs_to :measure, class_name: 'CQM::Measure', inverse_of: :calculation_result
+    belongs_to :patient, class_name: 'CQM::Patient', inverse_of: :calculation_result
 
     # Convert the stored array into a hash between clause and result
     def clause_results_by_clause

data/app/models/cqm/measure.rb

@@ -73,7 +73,7 @@ module CQM
     # hence the 'inverse_of: nil')
     has_and_belongs_to_many :value_sets, inverse_of: nil
 
-    has_many :calculation_results, class_name: 'CQM::IndividualResult'
+    has_many :calculation_results, class_name: 'CQM::IndividualResult', inverse_of: :measure
 
     def all_stratifications
       population_sets.flat_map(&:stratifications)

data/app/models/cqm/patient.rb

@@ -11,7 +11,7 @@ module CQM
 
     has_and_belongs_to_many :providers, class_name: 'CQM::Provider'
     embeds_one :qdmPatient, class_name: 'QDM::Patient', autobuild: true
-    has_many :calculation_results, class_name: 'CQM::IndividualResult'
+    has_many :calculation_results, class_name: 'CQM::IndividualResult', inverse_of: :patient
 
     # Include '_type' in any JSON output. This is necessary for deserialization.
     def to_json(options = nil)

data/app/models/cqm/provider.rb

@@ -12,8 +12,6 @@ module CQM
     field :specialty, type: String
     field :title, type: String
 
-    validates_uniqueness_of :npi, allow_blank: true
-
     embeds_many :addresses
     embeds_many :telecoms
     embeds_many :ids, class_name: 'QDM::Identifier'

data/app/models/qdm/attributes/identifier.rb

@@ -5,5 +5,7 @@ module QDM
     field :namingSystem, type: String
     field :value, type: String
     field :qdmVersion, type: String, default: '5.6'
+
+    validates_uniqueness_of :value, conditions: -> { where(namingSystem: CQM::Provider::NPI_OID) }
   end
 end

data/app/models/qdm/basetypes/data_element.rb

@@ -76,7 +76,9 @@ module QDM
         elsif field == 'facilityLocation'
           facility_location = send(field)
           unless facility_location.nil?
-            shift_facility_location_dates(facility_location, seconds)
+            # Guessing something changed in mongoid such that facility_location gets typed to an Object
+            # but this method (I think) expects a Hash.
+            shift_facility_location_dates(facility_location.attributes, seconds)
             send(field + '=', facility_location)
           end
         end

data/cqm-models.gemspec

@@ -4,7 +4,7 @@ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 
 Gem::Specification.new do |spec|
   spec.name          = 'cqm-models'
-  spec.version       = '4.1.1'
+  spec.version       = '4.2.0'
   spec.authors       = ['aholmes@mitre.org', 'mokeefe@mitre.org', 'lades@mitre.org']
 
   spec.summary       = 'Mongo models that correspond to the QDM specification.'
@@ -20,13 +20,13 @@ Gem::Specification.new do |spec|
   spec.require_paths = ['lib']
 
   spec.add_development_dependency 'bundle-audit'
-  spec.add_development_dependency 'bundler', '~> 2.1.4'
   spec.add_development_dependency 'byebug', '~> 11.0.1'
   spec.add_development_dependency 'codecov'
-  spec.add_development_dependency 'mongoid', '~> 6.4'
-  spec.add_development_dependency 'rails', '~> 5.2'
+  spec.add_development_dependency 'mongoid', '~> 8'
+  spec.add_development_dependency 'nokogiri', '>= 1.16.2'
+  spec.add_development_dependency 'rails', '~> 7.1'
   spec.add_development_dependency 'rake', '~> 12.3.3'
   spec.add_development_dependency 'rspec', '~> 3.0'
-  spec.add_development_dependency 'rubocop', '~> 0.54.0'
+  spec.add_development_dependency 'rubocop', '~> 0.63.0'
   spec.add_development_dependency 'simplecov'
 end