cqm-models 1.0.3 → 1.1.1.0

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

@@ -0,0 +1,30 @@
+const mongoose = require('mongoose/browser');
+
+const Code = require('../basetypes/Code');
+const Interval = require('../basetypes/Interval');
+const Quantity = require('../basetypes/Quantity');
+const DateTime = require('../basetypes/DateTime');
+const Any = require('../basetypes/Any');
+
+
+const [Number, String] = [
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+];
+
+const ComponentSchema = new mongoose.Schema({
+  code: Code,
+  result: Any,
+  qdmVersion: { type: String, default: '5.4' },
+  _type: { type: String, default: 'QDM::Component' },
+
+});
+
+module.exports.ComponentSchema = ComponentSchema;
+class Component extends mongoose.Document {
+  constructor(object) {
+    super(object, ComponentSchema);
+    this._type = 'QDM::Component';
+  }
+}
+module.exports.Component = Component;

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

@@ -0,0 +1,30 @@
+const mongoose = require('mongoose/browser');
+
+const Code = require('../basetypes/Code');
+const Interval = require('../basetypes/Interval');
+const Quantity = require('../basetypes/Quantity');
+const DateTime = require('../basetypes/DateTime');
+const Any = require('../basetypes/Any');
+
+
+const [Number, String] = [
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+];
+
+const FacilityLocationSchema = new mongoose.Schema({
+  code: Code,
+  locationPeriod: Interval,
+  qdmVersion: { type: String, default: '5.4' },
+  _type: { type: String, default: 'QDM::FacilityLocation' },
+
+});
+
+module.exports.FacilityLocationSchema = FacilityLocationSchema;
+class FacilityLocation extends mongoose.Document {
+  constructor(object) {
+    super(object, FacilityLocationSchema);
+    this._type = 'QDM::FacilityLocation';
+  }
+}
+module.exports.FacilityLocation = FacilityLocation;

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

@@ -1,4 +1,4 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 const cql = require('cql-execution');
 
 function Any(key, options) {

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

@@ -1,4 +1,4 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 const cql = require('cql-execution');
 
 function Code(key, options) {

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

@@ -1,4 +1,4 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 const Code = require('./Code.js');
 const cql = require('cql-execution');
 const Id = require('../Id');
@@ -9,6 +9,7 @@ function DataElementSchema(add, options) {
   const extended = new Schema({
     dataElementCodes: { type: [] },
     description: { type: String },
+    codeListId: { type: String },
     id: {
       type: Id.IdSchema,
       default() {

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

@@ -1,4 +1,4 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 const cql = require('cql-execution');
 
 function DateTime(key, options) {
@@ -7,6 +7,10 @@ function DateTime(key, options) {
 DateTime.prototype = Object.create(mongoose.SchemaType.prototype);
 
 DateTime.prototype.cast = (dateTime) => {
+  if (dateTime.isDateTime) {
+    return dateTime;
+  }
+
   if (!Date.parse(dateTime)) {
     throw new Error(`DateTime: ${dateTime} is not a valid DateTime`);
   }

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

@@ -1,4 +1,4 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 const cql = require('cql-execution');
 
 function Interval(key, options) {

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

@@ -1,4 +1,4 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 const cql = require('cql-execution');
 
 function Quantity(key, options) {

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

@@ -1,4 +1,4 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 const cql = require('cql-execution');
 
 function Ratio(key, options) {

data/app/assets/javascripts/browser.js

@@ -0,0 +1,3 @@
+window.cqm = window.cqm || {};
+window.cqm.models = require('./index');
+

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

@@ -0,0 +1,24 @@
+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.StatementDependency = require('./CQLStatementDependency.js').StatementDependency;
+module.exports.StatementDependencySchema = require('./CQLStatementDependency.js').StatementDependencySchema;
+module.exports.StatementReference = require('./CQLStatementDependency.js').StatementReference;
+module.exports.StatementReferenceSchema = require('./CQLStatementDependency.js').StatementReferenceSchema;
+module.exports.CQLLibrary = require('./CQLLibrary.js').CQLLibrary;
+module.exports.CQLLibrarySchema = require('./CQLLibrary.js').CQLLibrarySchema;
+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.PopulationSet = require('./PopulationSet.js').PopulationSet;
+module.exports.PopulationSetSchema = require('./PopulationSet.js').PopulationSetSchema;
+module.exports.PopulationMap = require('./PopulationSet.js').PopulationMap;
+module.exports.PopulationMapSchema = require('./PopulationSet.js').PopulationMapSchema;
+module.exports.Stratification = require('./PopulationSet.js').Stratification;
+module.exports.StratificationSchema = require('./PopulationSet.js').StratificationSchema;
+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;

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

@@ -0,0 +1,32 @@
+const mongoose = require('mongoose/browser');
+const { StatementDependencySchema } = require('./CQLStatementDependency');
+
+const [Mixed, mDate] = [
+  mongoose.Schema.Types.Mixed,
+  mongoose.Schema.Types.Date,
+];
+
+const CQLLibrarySchema = new mongoose.Schema(
+  {
+    library_name: String,
+    library_version: String,
+    cql: String,
+    elm: Mixed,
+    elm_annotations: Mixed,
+    is_main_library: { type: Boolean, default: false },
+    is_top_level: { type: Boolean, default: true },
+    statement_dependencies: [StatementDependencySchema],
+  },
+  // Options
+  {
+    timestamps: { createdAt: 'created_at', updatedAt: 'updated_at' }, // These are the Mongoid conventions for timestamps
+  }
+);
+
+module.exports.CQLLibrarySchema = CQLLibrarySchema;
+class CQLLibrary extends mongoose.Document {
+  constructor(object) {
+    super(object, CQLLibrarySchema);
+  }
+}
+module.exports.CQLLibrary = CQLLibrary;

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

@@ -0,0 +1,28 @@
+const mongoose = require('mongoose/browser');
+
+const StatementReferenceSchema = new mongoose.Schema({
+  library_name: String,
+  statement_name: String,
+  hqmf_id: String,
+});
+
+const StatementDependencySchema = new mongoose.Schema({
+  statement_name: String,
+  statement_references: [StatementReferenceSchema],
+});
+
+module.exports.StatementReferenceSchema = StatementReferenceSchema;
+class StatementReference extends mongoose.Document {
+  constructor(object) {
+    super(object, StatementReferenceSchema);
+  }
+}
+module.exports.StatementReference = StatementReference;
+
+module.exports.StatementDependencySchema = StatementDependencySchema;
+class StatementDependency extends mongoose.Document {
+  constructor(object) {
+    super(object, StatementDependencySchema);
+  }
+}
+module.exports.StatementDependency = StatementDependency;

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

@@ -0,0 +1,17 @@
+const mongoose = require('mongoose/browser');
+
+const ConceptSchema = new mongoose.Schema({
+  code: String,
+  code_system_oid: String,
+  code_system_name: String,
+  code_system_version: String,
+  display_name: String,
+});
+
+module.exports.ConceptSchema = ConceptSchema;
+class Concept extends mongoose.Document {
+  constructor(object) {
+    super(object, ConceptSchema);
+  }
+}
+module.exports.Concept = Concept;

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

@@ -0,0 +1,108 @@
+const mongoose = require('mongoose/browser');
+const Code = require('../basetypes/Code');
+const Interval = require('../basetypes/Interval');
+const Quantity = require('../basetypes/Quantity');
+const DataElementSchema = require('../basetypes/DataElement').DataElementSchema();
+const AllDataElements = require('../AllDataElements');
+const { CQLLibrarySchema } = require('./CQLLibrary');
+const { PopulationSetSchema } = require('./PopulationSet');
+
+const [Number, String, Boolean, Mixed, ObjectId, Date] = [
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+  mongoose.Schema.Types.Boolean,
+  mongoose.Schema.Types.Mixed,
+  mongoose.Schema.Types.ObjectId,
+  mongoose.Schema.Types.Date,
+];
+
+const MeasureSchema = new mongoose.Schema(
+  {
+    // A version-specific UUID for the measure
+    hqmf_id: String,
+    // A version-neutral UUID for the measure
+    hqmf_set_id: String,
+    // A Semantic Version-compliant string (e.g. "2.3.4") for the measure
+    hqmf_version_number: String,
+    // A CMS-style string (e.g. "CMS2v4") for the measure
+    cms_id: String,
+    title: String,
+    description: String,
+
+    // Composite/component measure fields
+    composite: {
+      type: Boolean,
+      default: false,
+    },
+    component: {
+      type: Boolean,
+      default: false,
+    },
+    component_hqmf_set_ids: [String],
+    composite_hqmf_set_id: String,
+
+    // Measure type variables
+    measure_scoring: {
+      type: String,
+      enum: ['PROPORTION', 'RATIO', 'CONTINUOUS_VARIABLE', 'COHORT'],
+      default: 'PROPORTION',
+    },
+    calculation_method: {
+      type: String,
+      enum: ['PATIENT', 'EPISODE_OF_CARE'],
+      default: 'PATIENT',
+    },
+    calculate_sdes: Boolean,
+
+    // ELM/CQL Measure-logic related data encapsulated in CQLLibrarySchema
+    // Field name changed from 'cql' to 'cql_libraries' because the semantics of
+    // embeds_many: cqls (on the Ruby side) sounded weird,
+    // and we wanted to keep the API consistent
+    cql_libraries: [CQLLibrarySchema],
+    main_cql_library: String,
+
+    // HQMF/Tacoma-specific Measure-logic related data
+    population_criteria: Mixed,
+    source_data_criteria: [],
+    measure_period: Interval,
+    measure_attributes: [],
+
+    population_sets: [PopulationSetSchema],
+
+    // Relations to other model classes
+    bundle: { type: ObjectId, ref: 'Bundle' }, // Cypress-specific, until we migrate the Bundle into cqm-models
+    package: { type: ObjectId, ref: 'MeasurePackage' }, // Bonnie-specific
+    patients: [{ type: ObjectId, ref: 'Patient', index: true }],
+
+    value_sets: [{ type: ObjectId, ref: 'ValueSet' }],
+  },
+  // Options
+  {
+    timestamps: { createdAt: 'created_at', updatedAt: 'updated_at' }, // These are the Mongoid conventions for timestamps
+  }
+);
+
+// After initialization of a Measure model, initialize every individual data element
+// to its respective Mongoose Model
+MeasureSchema.methods.initializeDataElements = function initializeDataElements() {
+  let typeStripped;
+  const sourceDataCriteriaInit = [];
+  this.source_data_criteria.forEach((element) => {
+    typeStripped = element._type.replace(/QDM::/, '');
+    sourceDataCriteriaInit.push(new AllDataElements[typeStripped](element));
+  });
+  this.set('source_data_criteria', sourceDataCriteriaInit);
+};
+
+MeasureSchema.methods.all_stratifications = function all_stratifications() {
+  return this.population_sets.flatMap(ps => ps.stratifications);
+};
+
+module.exports.MeasureSchema = MeasureSchema;
+class Measure extends mongoose.Document {
+  constructor(object) {
+    super(object, MeasureSchema);
+    this.initializeDataElements();
+  }
+}
+module.exports.Measure = Measure;

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

@@ -1,11 +1,12 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 
+// using mBuffer to not conflict with system Buffer
 const [mBuffer, ObjectId] = [
   mongoose.Schema.Types.Buffer,
   mongoose.Schema.Types.ObjectId,
 ];
 
-const MeasurePackageSchema = mongoose.Schema(
+const MeasurePackageSchema = new mongoose.Schema(
   {
     file: mBuffer,
     measure: { type: ObjectId, ref: 'Measure' },
@@ -17,4 +18,9 @@ const MeasurePackageSchema = mongoose.Schema(
 );
 
 module.exports.MeasurePackageSchema = MeasurePackageSchema;
-module.exports.MeasurePackage = mongoose.model('measure_package', MeasurePackageSchema);
+class MeasurePackage extends mongoose.Document {
+  constructor(object) {
+    super(object, MeasurePackageSchema);
+  }
+}
+module.exports.MeasurePackage = MeasurePackage;

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

@@ -0,0 +1,38 @@
+const mongoose = require('mongoose/browser');
+const Code = require('../basetypes/Code');
+const Interval = require('../basetypes/Interval');
+const Quantity = require('../basetypes/Quantity');
+const DateTime = require('../basetypes/DateTime');
+const { QDMPatientSchema, QDMPatient } = require('../QDMPatient');
+const { ProviderSchema } = require('./Provider');
+
+const [Schema, Number, String, Mixed] = [
+  mongoose.Schema,
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+  mongoose.Schema.Types.Mixed,
+];
+
+const PatientSchema = new Schema({
+
+  givenNames: [String],
+  familyName: String,
+  bundleId: String,
+  expectedValues: [],
+  notes: String,
+  qdmPatient: QDMPatientSchema,
+  providers: [ProviderSchema],
+  measure_ids: [String],
+
+}, { id: false });
+
+module.exports.PatientSchema = PatientSchema;
+class Patient extends mongoose.Document {
+  constructor(object) {
+    super(object, PatientSchema);
+    if (this.qdmPatient) {
+      this.qdmPatient = new QDMPatient(this.qdmPatient.toJSON());
+    }
+  }
+}
+module.exports.Patient = Patient;

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

@@ -0,0 +1,88 @@
+/* eslint-disable no-unused-vars, no-param-reassign */
+const mongoose = require('mongoose/browser');
+const { StatementReferenceSchema } = require('./CQLStatementDependency');
+
+const [Mixed] = [
+  mongoose.Schema.Types.Mixed,
+];
+
+// TODO: figure out if there is a better way to handle inheritance like mongoid.
+//  _type is how mongoid stores the specific type of the embedded document.
+const PopulationMapSchema = new mongoose.Schema({
+  _type: String,
+  IPP: StatementReferenceSchema,
+  DENOM: StatementReferenceSchema,
+  NUMER: StatementReferenceSchema,
+  NUMEX: StatementReferenceSchema,
+  DENEX: StatementReferenceSchema,
+  DENEXCEP: StatementReferenceSchema,
+  MSRPOPL: StatementReferenceSchema,
+  MSRPOPLEX: StatementReferenceSchema,
+  // STRAT is only here so cqm-execution can handle stratification results compliation with the current approach.
+  STRAT: StatementReferenceSchema,
+});
+
+if (!PopulationMapSchema.options.toObject) PopulationMapSchema.options.toObject = {};
+PopulationMapSchema.options.toObject.transform = function transform(doc, ret, options) {
+  // remove the _id and _type of every document before returning the result
+  delete ret._id;
+  delete ret._type;
+  return ret;
+};
+
+
+const StratificationSchema = new mongoose.Schema({
+  title: String,
+  stratification_id: String,
+  hqmf_id: String,
+  statement: StatementReferenceSchema,
+});
+
+const ObservationSchema = new mongoose.Schema({
+  title: String,
+  observation_function: StatementReferenceSchema,
+  observation_parameter: StatementReferenceSchema,
+  aggregation_type: String,
+  hqmf_id: String,
+});
+
+const PopulationSetSchema = new mongoose.Schema({
+  title: String,
+  population_set_id: String,
+  populations: PopulationMapSchema,
+  stratifications: [StratificationSchema],
+  supplemental_data_elements: [StatementReferenceSchema],
+  observations: [ObservationSchema],
+});
+
+module.exports.StratificationSchema = StratificationSchema;
+class Stratification extends mongoose.Document {
+  constructor(object) {
+    super(object, StratificationSchema);
+  }
+}
+module.exports.Stratification = Stratification;
+
+module.exports.ObservationSchema = ObservationSchema;
+class Observation extends mongoose.Document {
+  constructor(object) {
+    super(object, ObservationSchema);
+  }
+}
+module.exports.Observation = Observation;
+
+module.exports.PopulationMapSchema = PopulationMapSchema;
+class PopulationMap extends mongoose.Document {
+  constructor(object) {
+    super(object, PopulationMapSchema);
+  }
+}
+module.exports.PopulationMap = PopulationMap;
+
+module.exports.PopulationSetSchema = PopulationSetSchema;
+class PopulationSet extends mongoose.Document {
+  constructor(object) {
+    super(object, PopulationSetSchema);
+  }
+}
+module.exports.PopulationSet = PopulationSet;