cqm-models 1.0.3 → 1.1.1.0

data/app/assets/javascripts/cqm/Provider.js

@@ -0,0 +1,44 @@
+const mongoose = require('mongoose/browser');
+const Id = require('../Id');
+
+const [Schema, String, Boolean] = [
+  mongoose.Schema,
+  mongoose.Schema.Types.String,
+  mongoose.Schema.Types.Boolean,
+];
+
+const AddressSchema = new mongoose.Schema({
+  street: [String],
+  city: String,
+  state: String,
+  zip: String,
+  country: String,
+  use: String,
+});
+
+const TelecomSchema = new mongoose.Schema({
+  use: String,
+  value: String,
+  preferred: Boolean,
+});
+
+const ProviderSchema = new Schema({
+  _type: { type: String, default: 'Provider' },
+
+  givenNames: [String],
+  familyName: String,
+  specialty: String,
+  title: String,
+  addresses: [AddressSchema],
+  telecoms: [TelecomSchema],
+  ids: [Id.IdSchema],
+
+}, { id: false });
+
+module.exports.ProviderSchema = ProviderSchema;
+class Provider extends mongoose.Document {
+  constructor(object) {
+    super(object, ProviderSchema);
+  }
+}
+module.exports.Provider = Provider;

data/app/assets/javascripts/cqm/ValueSet.js

@@ -0,0 +1,26 @@
+const mongoose = require('mongoose/browser');
+const Concept = require('./Concept.js');
+
+const [String] = [mongoose.Schema.Types.String];
+
+const ValueSetSchema = new mongoose.Schema(
+  {
+    oid: String,
+    display_name: String,
+    version: String,
+
+    concepts: [Concept.ConceptSchema],
+  },
+  // Options
+  {
+    timestamps: { createdAt: 'created_at', updatedAt: 'updated_at' },
+  }
+);
+
+module.exports.ValueSetSchema = ValueSetSchema;
+class ValueSet extends mongoose.Document {
+  constructor(object) {
+    super(object, ValueSetSchema);
+  }
+}
+module.exports.ValueSet = ValueSet;

data/app/assets/javascripts/index.js

@@ -2,13 +2,23 @@ module.exports = require('./AllDataElements.js');
 module.exports.CQL = require('cql-execution');
 module.exports.Result = require('./Result.js').Result;
 module.exports.ResultSchema = require('./Result.js').ResultSchema;
-module.exports.Measure = require('./Measure.js').Measure;
-module.exports.MeasureSchema = require('./Measure.js').MeasureSchema;
-module.exports.MeasurePackage = require('./MeasurePackage.js').MeasurePackage;
-module.exports.MeasurePackageSchema = require('./MeasurePackage.js').MeasurePackageSchema;
-module.exports.ValueSet = require('./ValueSet.js').ValueSet;
-module.exports.ValueSetSchema = require('./ValueSet.js').ValueSetSchema;
-module.exports.Concept = require('./Concept.js').Concept;
-module.exports.ConceptSchema = require('./Concept.js').ConceptSchema;
+module.exports.Measure = require('./cqm/Measure.js').Measure;
+module.exports.MeasureSchema = require('./cqm/Measure.js').MeasureSchema;
+module.exports.MeasurePackage = require('./cqm/MeasurePackage.js').MeasurePackage;
+module.exports.MeasurePackageSchema = require('./cqm/MeasurePackage.js').MeasurePackageSchema;
+module.exports.Patient = require('./cqm/Patient.js').Patient;
+module.exports.PatientSchema = require('./cqm/Patient.js').PatientSchema;
+module.exports.Provider = require('./cqm/Provider.js').Provider;
+module.exports.ProviderSchema = require('./cqm/Provider.js').ProviderSchema;
+module.exports.StatementDependency = require('./cqm/CQLStatementDependency.js').StatementDependency;
+module.exports.StatementDependencySchema = require('./cqm/CQLStatementDependency.js').StatementDependencySchema;
+module.exports.PopulationSet = require('./cqm/PopulationSet.js').PopulationSet;
+module.exports.PopulationSetSchema = require('./cqm/PopulationSet.js').PopulationSetSchema;
+module.exports.CQLLibrary = require('./cqm/CQLLibrary.js').CQLLibrary;
+module.exports.CQLLibrarySchema = require('./cqm/CQLLibrary.js').CQLLibrarySchema;
+module.exports.ValueSet = require('./cqm/ValueSet.js').ValueSet;
+module.exports.ValueSetSchema = require('./cqm/ValueSet.js').ValueSetSchema;
+module.exports.Concept = require('./cqm/Concept.js').Concept;
+module.exports.ConceptSchema = require('./cqm/Concept.js').ConceptSchema;
 module.exports.IndividualResult = require('./IndividualResult').IndividualResult;
 module.exports.IndividualResultSchema = require('./IndividualResult').IndividualResultSchema;

data/app/models/{qdm/tacoma → cqm}/concept.rb

@@ -1,14 +1,14 @@
-module QDM
+module CQM
   # Concept is an individual code within a ValueSet, including all of the associated metadata
   # such as code system, version, and display name
   class Concept
     include Mongoid::Document
     field :code, type: String
+    field :code_system_oid, type: String
     field :code_system_name, type: String
     field :code_system_version, type: String
     field :display_name, type: String
-    field :code_system, type: String
-    scope :by_code_system_name, ->(cs) { where(code_system_name: cs) }
-    scope :by_code_system, ->(cs) { where(code_system: cs) }
+
+    embedded_in :value_set
   end
 end

data/app/models/cqm/cql_library.rb

@@ -0,0 +1,22 @@
+module CQM
+  # CQLLibrary encapsulates what used to be a Hash in Ruby, by explicitly specifying
+  # a library ID, and the CQL string for that library
+  class CQLLibrary
+    include Mongoid::Document
+    embedded_in :measure
+
+    field :library_name, type: String
+    field :library_version, type: String
+    field :cql, type: String
+    field :elm, type: Hash
+    field :elm_annotations, type: Hash
+    field :is_main_library, type: Boolean, default: false
+
+    # Currently this is only relevant for cql libraries that are included in composite measures,
+    # true indicates the library files are in the "top level" folder of the measure package, rather
+    # than coming from a component measure folder.
+    field :is_top_level, type: Boolean, default: true
+
+    embeds_many :statement_dependencies, class_name: 'CQM::StatementDependency'
+  end
+end

data/app/models/cqm/cql_statement_dependency.rb

@@ -0,0 +1,24 @@
+module CQM
+  # Statement is a given CQL Statement within a CQL Library, which has many dependencies
+  class StatementDependency
+    include Mongoid::Document
+    embedded_in :cql_library
+
+    field :statement_name, type: String
+    embeds_many :statement_references
+  end
+
+  # StatementReference notes a CQL Library/Statement which a given Statement (in which it is embedded) relies upon. This
+  # is also used for populations/stratifications/SDEs to reference their defining statement.
+  class StatementReference
+    include Mongoid::Document
+    embedded_in :statement_dependency
+    embedded_in :population_set
+    embedded_in :population_map
+    embedded_in :stratification
+
+    field :library_name, type: String
+    field :statement_name, type: String
+    field :hqmf_id, type: String
+  end
+end

data/app/models/cqm/measure.rb

@@ -0,0 +1,105 @@
+module CQM
+  # Measure contains the information necessary to represent the CQL version of a Clinical Quality Measure,
+  # As needed by the Bonnie & Cypress applications
+  class Measure
+    include Mongoid::Document
+    include Mongoid::Timestamps
+
+    # These are the Mongoid equivalent of the Mongoose "enum" attribute for the respective fields.
+    # They throw an error if you try to assign a value that's not in the array.
+    validates_inclusion_of :measure_scoring, in: %w[PROPORTION RATIO CONTINUOUS_VARIABLE COHORT]
+    validates_inclusion_of :calculation_method, in: %w[PATIENT EPISODE_OF_CARE]
+
+    IPP = 'IPP'.freeze
+    DENOM = 'DENOM'.freeze
+    NUMER = 'NUMER'.freeze
+    NUMEX = 'NUMEX'.freeze
+    DENEXCEP = 'DENEXCEP'.freeze
+    DENEX = 'DENEX'.freeze
+    MSRPOPL = 'MSRPOPL'.freeze
+    OBSERV = 'OBSERV'.freeze
+    MSRPOPLEX = 'MSRPOPLEX'.freeze
+
+    STRAT = 'STRAT'.freeze
+
+    ALL_POPULATION_CODES = [STRAT, IPP, DENOM, DENEX, NUMER, NUMEX, DENEXCEP, MSRPOPL, OBSERV, MSRPOPLEX].freeze
+
+    CQL_SKIP_STATEMENTS = ['SDE Ethnicity', 'SDE Payer', 'SDE Race', 'SDE Sex'].freeze
+
+    # A version-specific UUID for the measure
+    field :hqmf_id, type: String
+    # A version-neutral UUID for the measure
+    field :hqmf_set_id, type: String
+    # A Semantic Version-compliant string (e.g. "2.3.4") for the measure
+    field :hqmf_version_number, type: String
+    # A CMS-style string (e.g. "CMS2v4") for the measure
+    field :cms_id, type: String
+    field :title, type: String, default: ''
+    field :description, type: String, default: ''
+
+    # Composite/component measure fields
+    field :composite, type: Boolean, default: false
+    field :component, type: Boolean, default: false
+    field :component_hqmf_set_ids, type: Array, default: []
+    field :composite_hqmf_set_id, type: String
+
+    # Measure type variables
+    # Note: these are constrained to an enumeration of value options above, via validates_inclusion_of
+    field :measure_scoring, type: String, default: 'PROPORTION'
+    field :calculation_method, type: String, default: 'PATIENT'
+    field :calculate_sdes, type: Boolean
+
+    # ELM/CQL Measure-logic related data
+    # Field name changed from 'cql' to 'cql_libraries' because the semantics of
+    # embeds_many :cqls sounded weird
+    embeds_many :cql_libraries, class_name: 'CQM::CQLLibrary'
+    field :main_cql_library, type: String
+
+    # HQMF/Tacoma-specific Measure-logic related data
+    field :population_criteria, type: Hash
+    field :measure_period, type: Hash
+    field :measure_attributes, type: Array
+    embeds_many :source_data_criteria, class_name: 'QDM::DataElement'
+
+    embeds_many :population_sets
+
+    # Relations to other model classes
+    # Note: bundle is removed, Cypress may create their own bundle object and inject the relationship
+    has_one :package, class_name: 'CQM::MeasurePackage', inverse_of: :measure, dependent: :destroy # Bonnie-specific
+
+    # Store this references as an Array on the Measure object,
+    # but don't care about the inverse relationship (e.g. we never really care
+    # about getting all the measures from a ValueSet object,
+    # hence the 'inverse_of: nil')
+    has_and_belongs_to_many :value_sets, inverse_of: nil
+
+    def all_stratifications
+      population_sets.flat_map(&:stratifications)
+    end
+
+    # Returns the hqmf-parser's ruby implementation of an HQMF document.
+    # Rebuild from population_criteria, data_criteria, and measure_period JSON
+    def as_hqmf_model
+      json = {
+        'id' => hqmf_id,
+        'title' => title,
+        'description' => description,
+        'population_criteria' => population_criteria,
+        'data_criteria' => data_criteria,
+        'source_data_criteria' => source_data_criteria,
+        'measure_period' => measure_period,
+        'attributes' => measure_attributes,
+        'populations' => populations,
+        'hqmf_id' => hqmf_id,
+        'hqmf_set_id' => hqmf_set_id,
+        'hqmf_version_number' => hqmf_version_number,
+        'cms_id' => cms_id
+      }
+      HQMF::Document.from_json(json)
+    end
+
+    def all_data_criteria
+      as_hqmf_model.all_data_criteria
+    end
+  end
+end

data/app/models/{qdm/tacoma → cqm}/measure_package.rb

@@ -1,10 +1,10 @@
-module QDM
+module CQM
   # MeasurePackage stores the uploaded file for a given Measure, so it can be recreated if need be
   class MeasurePackage
     include Mongoid::Document
     include Mongoid::Timestamps
 
     field :file, type: BSON::Binary
-    belongs_to :measure, class_name: 'Measure', inverse_of: :package
+    belongs_to :measure, class_name: 'CQM::Measure', inverse_of: :package
   end
 end

data/app/models/cqm/patient.rb

@@ -0,0 +1,20 @@
+module CQM
+  # Patient model that holds non-QDM data for the patient
+  class Patient
+    include Mongoid::Document
+    field :givenNames, type: Array
+    field :familyName, type: String
+    field :bundleId, type: String
+    field :expectedValues, type: Array
+    field :notes, type: String
+    field :measure_ids, type: Array
+
+    has_and_belongs_to_many :providers, class_name: 'CQM::Provider'
+    embeds_one :qdmPatient, class_name: 'QDM::Patient', autobuild: true
+
+    # Include '_type' in any JSON output. This is necessary for deserialization.
+    def to_json(options = nil)
+      serializable_hash(include: :_type, methods: :_type).to_json(options)
+    end
+  end
+end

data/app/models/cqm/population_set.rb

@@ -0,0 +1,86 @@
+module CQM
+  # Representation of a population set (aka. PopulationCriteria)
+  class PopulationSet
+    include Mongoid::Document
+
+    embedded_in :measure
+
+    embeds_one :populations, class_name: 'CQM::PopulationMap'
+    embeds_many :stratifications
+    embeds_many :supplemental_data_elements, class_name: 'CQM::StatementReference'
+    embeds_many :observations
+
+    field :title, type: String
+    field :population_set_id, type: String
+  end
+
+  # Stratification info
+  class Stratification
+    include Mongoid::Document
+
+    embedded_in :population_set
+
+    field :title, type: String
+    field :stratification_id, type: String
+    field :hqmf_id, type: String
+    embeds_one :statement, class_name: 'CQM::StatementReference'
+  end
+
+  # Observation info
+  class Observation
+    include Mongoid::Document
+
+    embedded_in :population_set
+
+    embeds_one :observation_function, class_name: 'CQM::StatementReference'
+    embeds_one :observation_parameter, class_name: 'CQM::StatementReference'
+    field :aggregation_type, type: String
+    field :hqmf_id, type: String
+  end
+
+  # Base class for the population maps
+  class PopulationMap
+    include Mongoid::Document
+
+    embedded_in :population_set
+  end
+
+  # The population map for a porportion population set
+  class ProportionPopulationMap < PopulationMap
+    include Mongoid::Document
+
+    embeds_one :IPP, class_name: 'CQM::StatementReference'
+    embeds_one :DENOM, class_name: 'CQM::StatementReference'
+    embeds_one :NUMER, class_name: 'CQM::StatementReference'
+    embeds_one :NUMEX, class_name: 'CQM::StatementReference'
+    embeds_one :DENEX, class_name: 'CQM::StatementReference'
+    embeds_one :DENEXCEP, class_name: 'CQM::StatementReference'
+  end
+
+  # The population map for a ratio population set
+  class RatioPopulationMap < PopulationMap
+    include Mongoid::Document
+
+    embeds_one :IPP, class_name: 'CQM::StatementReference'
+    embeds_one :DENOM, class_name: 'CQM::StatementReference'
+    embeds_one :NUMER, class_name: 'CQM::StatementReference'
+    embeds_one :NUMEX, class_name: 'CQM::StatementReference'
+    embeds_one :DENEX, class_name: 'CQM::StatementReference'
+  end
+
+  # The population map for a continuous variable population set
+  class ContinuousVariablePopulationMap < PopulationMap
+    include Mongoid::Document
+
+    embeds_one :IPP, class_name: 'CQM::StatementReference'
+    embeds_one :MSRPOPL, class_name: 'CQM::StatementReference'
+    embeds_one :MSRPOPLEX, class_name: 'CQM::StatementReference'
+  end
+
+  # The population map for a cohort population set
+  class CohortPopulationMap < PopulationMap
+    include Mongoid::Document
+
+    embeds_one :IPP, class_name: 'CQM::StatementReference'
+  end
+end

data/app/models/cqm/provider.rb

@@ -0,0 +1,110 @@
+module CQM
+  # Provider model that holds non-QDM data for the provider. As well as indentifiers referenced in QDM
+  class Provider
+    include Mongoid::Document
+
+    NPI_OID = '2.16.840.1.113883.4.6'.freeze
+    TAX_ID_OID = '2.16.840.1.113883.4.2'.freeze
+    CCN_OID = '2.16.840.1.113883.4.336'.freeze
+
+    field :givenNames, type: Array
+    field :familyName, type: String
+    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::Id'
+
+    def npi=(an_npi)
+      cda_id_npi = ids.where(namingSystem: NPI_OID).first
+      if cda_id_npi
+        cda_id_npi.value = an_npi
+        cda_id_npi.save!
+      else
+        ids << QDM::Id.new(namingSystem: NPI_OID, value: an_npi)
+      end
+    end
+
+    def npi
+      cda_id_npi = ids.where(namingSystem: NPI_OID).first
+      cda_id_npi ? cda_id_npi.value : nil
+    end
+
+    def tin=(a_tin)
+      ids << QDM::Id.new(namingSystem: TAX_ID_OID, value: a_tin)
+    end
+
+    def tin
+      cda_id_tin = ids.where(namingSystem: TAX_ID_OID).first
+      cda_id_tin ? cda_id_tin.value : nil
+    end
+
+    def ccn=(a_ccn)
+      cda_id_ccn = ids.where(namingSystem: CCN_OID).first
+      if cda_id_ccn
+        cda_id_ccn.value = a_ccn
+        cda_id_ccn.save!
+      else
+        ids << QDM::Id.new(namingSystem: CCN_OID, value: a_ccn)
+      end
+    end
+
+    def ccn
+      cda_id_ccn = ids.where(namingSystem: CCN_OID).first
+      cda_id_ccn ? cda_id_ccn.value : nil
+    end
+
+    # validate the NPI, should be 10 or 15 digits total with the final digit being a
+    # checksum using the Luhn algorithm with additional special handling as described in
+    # https://www.cms.gov/NationalProvIdentStand/Downloads/NPIcheckdigit.pdf
+    def self.valid_npi?(npi)
+      return false unless npi
+      return false if npi.length != 10 && npi.length != 15
+      return false if npi.gsub(/\d/, '').length.positive? # npi must be all digits
+      return false if npi.length == 15 && (npi =~ /^80840/).nil? # 15 digit npi must start with 80840
+
+      # checksum is always calculated as if 80840 prefix is present
+      npi = '80840' + npi if npi.length == 10
+
+      luhn_checksum(npi[0, 14]) == npi[14]
+    end
+
+    def self.luhn_checksum(num)
+      double = { '0' => 0, '1' => 2, '2' => 4, '3' => 6, '4' => 8, '5' => 1, '6' => 3, '7' => 5, '8' => 7, '9' => 9 }
+      sum = 0
+      num.reverse!
+      num.split('').each_with_index do |char, i|
+        sum += if (i % 2).zero?
+                 double[char]
+               else
+                 char.to_i
+               end
+      end
+      sum = (9 * sum) % 10
+
+      sum.to_s
+    end
+  end
+
+  # Model for a standard postal address
+  class Address
+    include Mongoid::Document
+    field :street, type: Array, default: []
+    field :city, type: String
+    field :state, type: String
+    field :zip, type: String
+    field :country, type: String
+    field :use, type: String
+  end
+
+  # Model for a standard telephone number
+  class Telecom
+    include Mongoid::Document
+    field :use, type: String
+    field :value, type: String
+    field :preferred, type: Boolean
+  end
+end