cqm-models 1.1.1.0 → 2.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -3,7 +3,7 @@ matrix:
     - language: ruby
       cache: bundler
       rvm:
-        - 2.4.1
+        - 2.4.6
       services:
         - mongodb
       before_install:

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

@@ -10,20 +10,19 @@ function RecursiveCast(any) {
   if (any && any.value && any.unit) {
     return new cql.Quantity(any);
   }
-  if (any && any.code && any.codeSystem) {
+  if (any && any.code && (any.codeSystemOid || any.system)) {
     if (typeof any.code === 'undefined') {
       throw new Error(`Code: ${any} does not have a code`);
-    } else if (typeof any.codeSystem === 'undefined') {
-      throw new Error(`Code: ${any} does not have a codeSystem`);
+    } else if (typeof any.codeSystemOid === 'undefined' && typeof any.system === 'undefined') {
+      throw new Error(`Code: ${any} does not have a code system oid`);
     }
 
-    const val = { code: any.code, codeSystem: any.codeSystem };
+    const val = { code: any.code, codeSystemOid: any.codeSystemOid || any.system };
 
     val.descriptor = (typeof any.descriptor !== 'undefined') ? any.descriptor : null;
-    val.codeSystemOid = (typeof any.codeSystemOid !== 'undefined') ? any.codeSystemOid : null;
     val.version = (typeof any.version !== 'undefined') ? any.version : null;
 
-    return new cql.Code(val.code, val.codeSystem, val.version, val.descriptor);
+    return new cql.Code(val.code, val.codeSystemOid, val.version, val.descriptor);
   }
   if (any && any.low) {
     const casted = new cql.Interval(any.low, any.high, any.lowClosed, any.highClosed);

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

@@ -9,20 +9,19 @@ Code.prototype = Object.create(mongoose.SchemaType.prototype);
 Code.prototype.cast = (code) => {
   if (code != null) {
     // handles codes that have not yet been cast to a code and those that have already been cast to a code
-    if (code.code && (code.codeSystem || code.system)) {
+    if (code.code && (code.codeSystemOid || code.system)) {
       if (typeof code.code === 'undefined') {
         throw new Error(`Code: ${code} does not have a code`);
-      } else if (typeof code.codeSystem === 'undefined' && typeof code.system === 'undefined') {
-        throw new Error(`Code: ${code} does not have a system`);
+      } else if (typeof code.codeSystemOid === 'undefined' && typeof code.system === 'undefined') {
+        throw new Error(`Code: ${code} does not have a system oid`);
       }
 
-      const val = { code: code.code, codeSystem: code.codeSystem || code.system };
+      const val = { code: code.code, codeSystemOid: code.codeSystemOid || code.system };
 
       val.descriptor = (typeof code.descriptor !== 'undefined') ? code.descriptor : null;
-      val.codeSystemOid = (typeof code.codeSystemOid !== 'undefined') ? code.codeSystemOid : null;
       val.version = (typeof code.version !== 'undefined') ? code.version : null;
 
-      return new cql.Code(val.code, val.codeSystem, val.version, val.descriptor);
+      return new cql.Code(val.code, val.codeSystemOid, val.version, val.descriptor);
     }
     throw new Error(`Expected a code. Received ${code}.`);
   } else {

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

@@ -25,7 +25,7 @@ function DataElementSchema(add, options) {
   // Returns all of the codes on this data element in a format usable by
   // the cql-execution framework.
   extended.methods.getCode = function getCode() {
-    return this.dataElementCodes.map(code => new cql.Code(code.code, code.codeSystem, code.version, code.descriptor));
+    return this.dataElementCodes.map(code => new cql.Code(code.code, code.codeSystemOid, code.version, code.descriptor));
   };
 
   // Return the first code on this data element in a format usable by
@@ -33,7 +33,7 @@ function DataElementSchema(add, options) {
   extended.methods.code = function code() {
     if (this.dataElementCodes && this.dataElementCodes[0]) {
       const qdmCode = this.dataElementCodes[0];
-      return new cql.Code(qdmCode.code, qdmCode.codeSystem, qdmCode.version, qdmCode.descriptor);
+      return new cql.Code(qdmCode.code, qdmCode.codeSystemOid, qdmCode.version, qdmCode.descriptor);
     }
     return null;
   };

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

@@ -1,5 +1,6 @@
 const mongoose = require('mongoose/browser');
 const cql = require('cql-execution');
+const DateTime = require('./DateTime');
 
 function Interval(key, options) {
   mongoose.SchemaType.call(this, key, options, 'Interval');
@@ -7,8 +8,8 @@ function Interval(key, options) {
 Interval.prototype = Object.create(mongoose.SchemaType.prototype);
 
 Interval.prototype.cast = (interval) => {
-  if (typeof interval.low === 'undefined' || interval.low === null) {
-    throw new Error(`Interval: ${interval} does not have a low value`);
+  if (interval.isInterval) {
+    return interval;
   }
   const casted = new cql.Interval(interval.low, interval.high, interval.lowClosed, interval.highClosed);
 
@@ -22,11 +23,12 @@ Interval.prototype.cast = (interval) => {
   }
 
   // Cast to DateTime if it is a string representing a DateTime
-  if (casted.low && Date.parse(casted.low)) {
-    casted.low = cql.DateTime.fromJSDate(new Date(casted.low), 0);
+  if (casted.low) {
+    casted.low = DateTime.prototype.cast(casted.low);
   }
-  if (casted.high && Date.parse(casted.high)) {
-    casted.high = cql.DateTime.fromJSDate(new Date(casted.high), 0);
+
+  if (casted.high) {
+    casted.high = DateTime.prototype.cast(casted.high);
   }
   return casted;
 };

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

@@ -22,3 +22,5 @@ module.exports.Patient = require('./Patient.js').Patient;
 module.exports.PatientSchema = require('./Patient.js').PatientSchema;
 module.exports.Provider = require('./Provider.js').Provider;
 module.exports.ProviderSchema = require('./Provider.js').ProviderSchema;
+module.exports.IndividualResult = require('./IndividualResult.js').IndividualResult;
+module.exports.IndividualResultSchema = require('./IndividualResult.js').IndividualResultSchema;

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

@@ -0,0 +1,28 @@
+const mongoose = require('mongoose/browser');
+
+const [String, Mixed] = [
+  mongoose.Schema.Types.String,
+  mongoose.Schema.Types.Mixed,
+];
+
+const ClauseResultSchema = mongoose.Schema({
+  // Library the clause this result is for is in
+  library_name: String,
+  // Statement the clause this result is for is in
+  statement_name: String,
+  // LocalId of the clause this result is for
+  localId: String,
+  // Final, processed result of raw calculation
+  final: String,
+  // Raw result of clause calculation
+  raw: Mixed,
+});
+
+
+module.exports.ClauseResultSchema = ClauseResultSchema;
+class ClauseResult extends mongoose.Document {
+  constructor(object) {
+    super(object, ClauseResultSchema);
+  }
+}
+module.exports.ClauseResult = ClauseResult;

data/app/assets/javascripts/{IndividualResult.js → cqm/IndividualResult.js}

@@ -1,4 +1,6 @@
 const mongoose = require('mongoose/browser');
+const { ClauseResultSchema } = require('./ClauseResult');
+const { StatementResultSchema } = require('./StatementResult');
 
 const [Number, String, Mixed, ObjectId] = [
   mongoose.Schema.Types.Number,
@@ -22,9 +24,11 @@ const IndividualResultSchema = mongoose.Schema(
     MSRPOPLEX: Number,
 
     // Result Attributes
-    clause_results: Mixed,
+    clause_results: [ClauseResultSchema],
+    statement_results: [StatementResultSchema],
+    population_relevance: Mixed,
     episode_results: Mixed,
-    statement_results: Mixed,
+    observation_values: [Number],
 
     // This field is for application specific information only. If both Bonnie and
     // Cypress use a common field, it should be made a field on this model,
@@ -53,6 +57,28 @@ const IndividualResultSchema = mongoose.Schema(
   }
 );
 
+IndividualResultSchema.methods.clause_results_by_clause = function clause_results_by_clause() {
+  const clause_results_hash = {};
+  this.clause_results.forEach((result) => {
+    if (!clause_results_hash[result.library_name]) {
+      clause_results_hash[result.library_name] = {};
+    }
+    clause_results_hash[result.library_name][result.localId] = result;
+  });
+  return clause_results_hash;
+};
+
+IndividualResultSchema.methods.statement_results_by_statement = function statement_results_by_statement() {
+  const statement_results_hash = {};
+  this.statement_results.forEach((result) => {
+    if (!statement_results_hash[result.library_name]) {
+      statement_results_hash[result.library_name] = {};
+    }
+    statement_results_hash[result.library_name][result.statement_name] = result;
+  });
+  return statement_results_hash;
+};
+
 module.exports.IndividualResultSchema = IndividualResultSchema;
 class IndividualResult extends mongoose.Document {
   constructor(object) {

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

@@ -64,7 +64,7 @@ const MeasureSchema = new mongoose.Schema(
     // HQMF/Tacoma-specific Measure-logic related data
     population_criteria: Mixed,
     source_data_criteria: [],
-    measure_period: Interval,
+    measure_period: Mixed,
     measure_attributes: [],
 
     population_sets: [PopulationSetSchema],

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

@@ -0,0 +1,41 @@
+const mongoose = require('mongoose/browser');
+
+const [String, Mixed] = [
+  mongoose.Schema.Types.String,
+  mongoose.Schema.Types.Mixed,
+];
+
+const StatementResultSchema = mongoose.Schema({
+  // Library the statement this result is for is in
+  library_name: String,
+  // Statement this result is for is in
+  statement_name: String,
+  // Result, processed for display, of the statement this result is for
+  pretty: String,
+  // Final, processed result of raw calculation
+  final: String,
+  // Raw result of clause calculation
+  raw: Mixed,
+  /*
+   * 'NA' - Not applicable. This statement is not relevant to any population calculation in this population_set. Common
+   *   for unused library statements or statements only used for other population sets.
+   *
+   * 'FALSE' - This statement is not relevant to any of this patient's population inclusion calculations.
+   *
+   * 'TRUE' - This statement is relevant for one or more of the population inclusion calculations.
+    */
+  relevance: {
+    type: String,
+    enum: ['NA', 'TRUE', 'FALSE'],
+    default: 'NA',
+  },
+});
+
+
+module.exports.StatementResultSchema = StatementResultSchema;
+class StatementResult extends mongoose.Document {
+  constructor(object) {
+    super(object, StatementResultSchema);
+  }
+}
+module.exports.StatementResult = StatementResult;

data/app/assets/javascripts/index.js

@@ -20,5 +20,9 @@ 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;
+module.exports.IndividualResult = require('./cqm/IndividualResult.js').IndividualResult;
+module.exports.IndividualResultSchema = require('./cqm/IndividualResult.js').IndividualResultSchema;
+module.exports.ClauseResult = require('./cqm/ClauseResult.js').ClauseResult;
+module.exports.ClauseResultSchema = require('./cqm/ClauseResult.js').ClauseResultSchema;
+module.exports.StatementResult = require('./cqm/StatementResult.js').StatementResult;
+module.exports.StatementResultSchema = require('./cqm/StatementResult.js').StatementResultchema;

data/app/models/cqm/clause_result.rb

@@ -0,0 +1,21 @@
+module CQM
+  # ClauseResult is used to store clause result information in IndividualResult
+  class ClauseResult
+    include Mongoid::Document
+    include Mongoid::Timestamps
+
+    # Library the clause this result is for is in
+    field :library_name, type: String
+    # Statment the clause this result is for is in
+    field :statement_name, type: String
+    # LocalId of the clause this result is for
+    field :localId, type: String
+    # Final, processed result of raw calculation
+    field :final, type: String
+    # Raw result of clause calculation
+    field :raw
+
+    # Relations to other model classes
+    embedded_in :individual_result
+  end
+end

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

@@ -1,4 +1,4 @@
-module QDM
+module CQM
   # IndividualResult stores the patient-level (population/clause) results for a patient/measure combination
   class IndividualResult
     include Mongoid::Document
@@ -20,9 +20,11 @@ module QDM
     field :MSRPOPLEX, type: Integer
 
     # Result Attributes
-    field :clause_results, type: Hash
+    embeds_many :clause_results
+    embeds_many :statement_results
     field :episode_results, type: Hash
-    field :statement_results, type: Hash
+    field :observation_values, type: Array, default: []
+    field :population_relevance, type: Hash
 
     # This field is for application specific information only. If both Bonnie and
     # Cypress use a common field, it should be made a field on this model,
@@ -35,5 +37,28 @@ module QDM
     # Relations to other model classes
     belongs_to :measure
     belongs_to :patient
+
+    # Convert the stored array into a hash between clause and result
+    def clause_results_by_clause
+      clause_results_hash = {}
+      clause_results.each do |result|
+        unless clause_results_hash[result['library_name']]
+          clause_results_hash[result['library_name']] = {}
+        end
+        clause_results_hash[result['library_name']][result['localId']] = result
+      end
+      return clause_results_hash
+    end
+
+    def statement_results_by_statement
+      statement_results_hash = {}
+      statement_results.each do |result|
+        unless statement_results_hash[result['library_name']]
+          statement_results_hash[result['library_name']] = {}
+        end
+        statement_results_hash[result['library_name']][result['statement_name']] = result
+      end
+      return statement_results_hash
+    end
   end
 end

data/app/models/cqm/measure.rb

@@ -73,6 +73,8 @@ 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'
+
     def all_stratifications
       population_sets.flat_map(&:stratifications)
     end

data/app/models/cqm/patient.rb

@@ -11,6 +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'
 
     # Include '_type' in any JSON output. This is necessary for deserialization.
     def to_json(options = nil)

data/app/models/cqm/statement_result.rb

@@ -0,0 +1,27 @@
+module CQM
+  # StatementResult is used to store statement result information in IndividualResult
+  class StatementResult
+    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 :relevance, in: %w[NA TRUE FALSE]
+
+    # Library the clause this result is for is in
+    field :library_name, type: String
+    # Statment the clause this result is for is in
+    field :statement_name, type: String
+    # LocalId of the clause this result is for
+    field :pretty, type: String
+    # Final, processed result of raw calculation
+    field :final, type: String
+    # Raw result of clause calculation
+    field :raw
+
+    field :relevance, type: String
+
+    # Relations to other model classes
+    embedded_in :individual_result
+  end
+end

data/app/models/models.rb

@@ -29,7 +29,9 @@ require_relative 'cqm/cql_library'
 require_relative 'cqm/population_set'
 require_relative 'cqm/patient'
 require_relative 'cqm/provider'
-require_relative 'qdm/tacoma/individual_result'
+require_relative 'cqm/individual_result'
+require_relative 'cqm/statement_result'
+require_relative 'cqm/clause_result'
 
 # Make Patient Generation Available
 require_relative '../../lib/generate_patients'

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

@@ -4,7 +4,7 @@ module QDM
     attr_accessor :code, :codeSystem, :descriptor, :codeSystemOid, :version
 
     # Code and code system are required (at minimum).
-    def initialize(code, codeSystem, descriptor = nil, codeSystemOid = nil, version = nil)
+    def initialize(code, codeSystemOid, descriptor = nil, codeSystem = nil, version = nil)
       @code = code
       @codeSystem = codeSystem
       @descriptor = descriptor
@@ -14,7 +14,7 @@ module QDM
 
     # Converts an object of this instance into a database friendly value.
     def mongoize
-      { code: @code, codeSystem: @codeSystem, descriptor: @descriptor, codeSystemOid: @codeSystemOid, version: @version, _type: 'QDM::Code' }
+      { code: @code, codeSystemOid: @codeSystemOid, descriptor: @descriptor, codeSystem: @codeSystem, version: @version, _type: 'QDM::Code' }
     end
 
     class << self
@@ -26,7 +26,7 @@ module QDM
       def demongoize(object)
         return nil unless object
         object = object.symbolize_keys
-        QDM::Code.new(object[:code], object[:codeSystem], object[:descriptor], object[:codeSystemOid], object[:version])
+        QDM::Code.new(object[:code], object[:codeSystemOid], object[:descriptor], object[:codeSystem], object[:version])
       end
 
       # Takes any possible object and converts it to how it would be
@@ -37,8 +37,8 @@ module QDM
         when QDM::Code then object.mongoize
         when Hash
           object = object.symbolize_keys
-          codeSystem = object[:system] ? object[:system] : object[:codeSystem]
-          QDM::Code.new(object[:code], codeSystem, object[:descriptor], object[:codeSystemOid], object[:version]).mongoize
+          codeSystemOid = object[:system] ? object[:system] : object[:codeSystemOid]
+          QDM::Code.new(object[:code], codeSystemOid, object[:descriptor], object[:codeSystem], object[:version]).mongoize
         else object
         end
       end