cqm-models 2.0.0 → 3.0.3

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

@@ -0,0 +1,31 @@
+const mongoose = require('mongoose/browser');
+
+const { ComponentSchemaFunction } = require('./Component');
+const Code = require('../basetypes/Code');
+const Interval = require('../basetypes/Interval');
+const Quantity = require('../basetypes/Quantity');
+const DateTime = require('../basetypes/DateTime');
+const QDMDate = require('../basetypes/QDMDate');
+const Any = require('../basetypes/Any');
+
+const [Number, String] = [
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+];
+
+const ResultComponentSchema = ComponentSchemaFunction({
+  referenceRange: Interval,
+  _type: { type: String, default: 'QDM::ResultComponent' },
+
+});
+
+module.exports.ResultComponentSchema = ResultComponentSchema;
+class ResultComponent extends mongoose.Document {
+  constructor(object) {
+    super(object, ResultComponentSchema);
+    this._type = 'QDM::ResultComponent';
+  }
+}
+
+module.exports.ResultComponent = ResultComponent;
+

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

@@ -8,30 +8,31 @@ Any.prototype = Object.create(mongoose.SchemaType.prototype);
 
 function RecursiveCast(any) {
   if (any && any.value && any.unit) {
-    return new cql.Quantity(any);
+    return new cql.Quantity(any.value, any.unit);
   }
-  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.codeSystemOid === 'undefined' && typeof any.system === 'undefined') {
-      throw new Error(`Code: ${any} does not have a code system oid`);
-    }
 
-    const val = { code: any.code, codeSystemOid: any.codeSystemOid || any.system };
+  if (any.isCode || any.isConcept || any.isValueSet || any.isList ||
+      any.isDateTime || any.isDate || any.isRatio || any.isQuantiy ||
+      any.isInterval || any.isBooleanLiteral || any.isIntegerLiteral ||
+      any.isDecimalLiteral || any.isStringLiteral || any.isTuple) {
+    return any;
+  }
 
-    val.descriptor = (typeof any.descriptor !== 'undefined') ? any.descriptor : null;
+  if (any && any.code && any.system) {
+    const val = { code: any.code, system: any.system };
+    val.display = (typeof any.display !== 'undefined') ? any.display : null;
     val.version = (typeof any.version !== 'undefined') ? any.version : null;
 
-    return new cql.Code(val.code, val.codeSystemOid, val.version, val.descriptor);
+    return new cql.Code(val.code, val.system, val.version, val.display);
   }
   if (any && any.low) {
     const casted = new cql.Interval(any.low, any.high, any.lowClosed, any.highClosed);
 
     // Cast Low and High values to Quantities if it is a quantity
     if (casted.low && casted.low.unit && casted.low.value) {
-      casted.low = new cql.Quantity(casted.low);
+      casted.low = new cql.Quantity(casted.low.value, casted.low.unit);
       if (casted.high && casted.high.unit && casted.high.value) {
-        casted.high = new cql.Quantity(casted.high);
+        casted.high = new cql.Quantity(casted.high.value, casted.high.unit);
       }
       return casted;
     }
@@ -55,8 +56,17 @@ function RecursiveCast(any) {
   if (Number.isFinite(any)) {
     return any;
   }
-  if (Date.parse(any)) {
-    return cql.DateTime.fromJSDate(new Date(any), 0);
+  if (Date.parse(any) || Date.parse(`1984-01-01T${any}`)) {
+    if (any.match(/T/) || any.match(/\+/)) {
+      // If it has a T or a timezoneoffset, it must be a DateTime
+      return cql.DateTime.fromJSDate(new Date(any), 0);
+    }
+    if (any.match(/:/)) {
+      // If it has a : but no T or timezoneoffset, it must be a Time
+      return cql.DateTime.fromJSDate(new Date(`1984-01-01T${any}`), 0).getTime();
+    }
+    // Must be a Date
+    return cql.DateTime.fromJSDate(new Date(any), 0).getDate();
   }
   return any;
 }

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

@@ -0,0 +1,44 @@
+const mongoose = require('mongoose/browser');
+const { PatientEntity } = require('../attributes/PatientEntity');
+const { Practitioner } = require('../attributes/Practitioner');
+const { CarePartner } = require('../attributes/CarePartner');
+const { Organization } = require('../attributes/Organization');
+
+function AnyEntity(key, options) {
+  mongoose.SchemaType.call(this, key, options, 'AnyEntity');
+}
+AnyEntity.prototype = Object.create(mongoose.SchemaType.prototype);
+
+AnyEntity.prototype.cast = (entity) => {
+  if (entity == null) {
+    return null;
+  }
+
+  if (entity instanceof PatientEntity || entity instanceof Practitioner || entity instanceof CarePartner || entity instanceof Organization) {
+    return entity;
+  }
+
+  if (entity._type != null) {
+    // copy _id to id if it isn't defined
+    if (entity.id == null && entity._id != null) {
+      entity.id = entity._id;
+    }
+    switch (entity._type) {
+      case 'QDM::PatientEntity':
+        return new PatientEntity(entity);
+      case 'QDM::Practitioner':
+        return new Practitioner(entity);
+      case 'QDM::CarePartner':
+        return new CarePartner(entity);
+      case 'QDM::Organization':
+        return new Organization(entity);
+      default:
+        throw new Error(`Could not find entity type "${entity._type}".`);
+    }
+  } else {
+    throw new Error('Could not find _type indicator for entity.');
+  }
+};
+
+mongoose.Schema.Types.AnyEntity = AnyEntity;
+module.exports = AnyEntity;

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

@@ -8,20 +8,17 @@ Code.prototype = Object.create(mongoose.SchemaType.prototype);
 
 Code.prototype.cast = (code) => {
   if (code != null) {
+    // return code if it doesn't even need casting
+    if (code.isCode) {
+      return code;
+    }
     // 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.codeSystemOid || code.system)) {
-      if (typeof code.code === 'undefined') {
-        throw new Error(`Code: ${code} does not have a code`);
-      } 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, codeSystemOid: code.codeSystemOid || code.system };
-
-      val.descriptor = (typeof code.descriptor !== 'undefined') ? code.descriptor : null;
+    if (code.code && code.system) {
+      const val = { code: code.code, system: code.system };
+      val.display = (typeof code.display !== 'undefined') ? code.display : null;
       val.version = (typeof code.version !== 'undefined') ? code.version : null;
 
-      return new cql.Code(val.code, val.codeSystemOid, val.version, val.descriptor);
+      return new cql.Code(val.code, val.system, val.version, val.display);
     }
     throw new Error(`Expected a code. Received ${code}.`);
   } else {

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

@@ -1,19 +1,19 @@
 const mongoose = require('mongoose/browser');
 const Code = require('./Code.js');
 const cql = require('cql-execution');
-const Id = require('../Id');
+const Identifier = require('../attributes/Identifier');
 
 const [Schema] = [mongoose.Schema];
 
 function DataElementSchema(add, options) {
   const extended = new Schema({
-    dataElementCodes: { type: [] },
+    dataElementCodes: { type: [Code] },
     description: { type: String },
     codeListId: { type: String },
     id: {
-      type: Id.IdSchema,
+      type: String,
       default() {
-        return new Id.Id({ value: (this._id ? this._id.toString() : mongoose.Types.ObjectId().toString()), namingSystem: null });
+        return this._id ? this._id.toString() : mongoose.Types.ObjectId().toString();
       },
     },
   }, options);
@@ -25,7 +25,15 @@ 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.codeSystemOid, code.version, code.descriptor));
+    if (this.dataElementCodes) {
+      return this.dataElementCodes.map((code) => {
+        if (code.isCode) {
+          return code;
+        }
+        return new cql.Code(code.code, code.system, code.version, code.display);
+      });
+    }
+    return null;
   };
 
   // Return the first code on this data element in a format usable by
@@ -33,7 +41,10 @@ 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.codeSystemOid, qdmCode.version, qdmCode.descriptor);
+      if (qdmCode.isCode) {
+        return qdmCode;
+      }
+      return new cql.Code(qdmCode.code, qdmCode.system, qdmCode.version, qdmCode.display);
     }
     return null;
   };

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

@@ -15,9 +15,9 @@ Interval.prototype.cast = (interval) => {
 
   // Cast Low and High values to Quantities if it is a quantity
   if (casted.low && casted.low.unit && casted.low.value) {
-    casted.low = new cql.Quantity(casted.low);
+    casted.low = new cql.Quantity(casted.low.value, casted.low.unit);
     if (casted.high && casted.high.unit && casted.high.value) {
-      casted.high = new cql.Quantity(casted.high);
+      casted.high = new cql.Quantity(casted.high.value, casted.high.unit);
     }
     return casted;
   }

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

@@ -0,0 +1,36 @@
+const mongoose = require('mongoose/browser');
+const cql = require('cql-execution');
+
+function QDMDate(key, options) {
+  mongoose.SchemaType.call(this, key, options, 'Date');
+}
+QDMDate.prototype = Object.create(mongoose.SchemaType.prototype);
+
+QDMDate.prototype.cast = (date) => {
+  if (date == null) {
+    return date;
+  }
+
+  // Already a CQL Date
+  if (date.isDate) {
+    return date;
+  }
+
+  // Object
+  if (typeof date === 'object') {
+    const keys = Object.keys(date);
+    if (keys.includes('year') && keys.includes('month') && keys.includes('day')) {
+      return new cql.Date(date.year, date.month, date.day);
+    }
+  }
+
+  // Date String
+  if (!cql.Date.parse(date)) {
+    throw new Error(`Date: ${date} is not a valid Date`);
+  } else {
+    return cql.Date.parse(date);
+  }
+};
+
+mongoose.Schema.Types.QDMDate = QDMDate;
+module.exports = QDMDate;

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

@@ -13,7 +13,7 @@ Quantity.prototype.cast = (quantity) => {
     throw new Error(`Quantity: ${quantity} does not have a unit`);
   }
 
-  return new cql.Quantity(quantity);
+  return new cql.Quantity(quantity.value, quantity.unit);
 };
 
 mongoose.Schema.Types.Quantity = Quantity;

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

@@ -13,7 +13,7 @@ Ratio.prototype.cast = (ratio) => {
     throw new Error(`Ratio: ${ratio} does not have a denominator`);
   }
 
-  return new cql.Ratio(ratio);
+  return new cql.Ratio(ratio.numerator, ratio.denominator);
 };
 
 mongoose.Schema.Types.Ratio = Ratio;

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

@@ -1,5 +1,4 @@
 const mongoose = require('mongoose/browser');
-const Id = require('../Id');
 
 const [Schema, String, Boolean] = [
   mongoose.Schema,
@@ -31,7 +30,6 @@ const ProviderSchema = new Schema({
   title: String,
   addresses: [AddressSchema],
   telecoms: [TelecomSchema],
-  ids: [Id.IdSchema],
 
 }, { id: false });
 

data/app/models/cqm/individual_result.rb

@@ -42,9 +42,7 @@ module CQM
     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']] = {} unless clause_results_hash[result['library_name']]
         clause_results_hash[result['library_name']][result['localId']] = result
       end
       return clause_results_hash
@@ -53,9 +51,7 @@ module CQM
     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']] = {} unless statement_results_hash[result['library_name']]
         statement_results_hash[result['library_name']][result['statement_name']] = result
       end
       return statement_results_hash

data/app/models/cqm/provider.rb

@@ -16,7 +16,7 @@ module CQM
 
     embeds_many :addresses
     embeds_many :telecoms
-    embeds_many :ids, class_name: 'QDM::Id'
+    embeds_many :ids, class_name: 'QDM::Identifier'
 
     def npi=(an_npi)
       cda_id_npi = ids.where(namingSystem: NPI_OID).first
@@ -24,7 +24,7 @@ module CQM
         cda_id_npi.value = an_npi
         cda_id_npi.save!
       else
-        ids << QDM::Id.new(namingSystem: NPI_OID, value: an_npi)
+        ids << QDM::Identifier.new(namingSystem: NPI_OID, value: an_npi)
       end
     end
 
@@ -34,7 +34,7 @@ module CQM
     end
 
     def tin=(a_tin)
-      ids << QDM::Id.new(namingSystem: TAX_ID_OID, value: a_tin)
+      ids << QDM::Identifier.new(namingSystem: TAX_ID_OID, value: a_tin)
     end
 
     def tin
@@ -48,7 +48,7 @@ module CQM
         cda_id_ccn.value = a_ccn
         cda_id_ccn.save!
       else
-        ids << QDM::Id.new(namingSystem: CCN_OID, value: a_ccn)
+        ids << QDM::Identifier.new(namingSystem: CCN_OID, value: a_ccn)
       end
     end
 

data/app/models/hqmfOid_to_datatype_map.json

@@ -1,4 +1,9 @@
 {
+  "2.16.840.1.113883.10.20.28.4.136": "PatientEntity",
+  "2.16.840.1.113883.10.20.28.4.134": "CarePartner",
+  "2.16.840.1.113883.10.20.28.4.141": "RelatedPerson",
+  "2.16.840.1.113883.10.20.28.4.137": "Practitioner",
+  "2.16.840.1.113883.10.20.28.4.135": "Organization",
   "2.16.840.1.113883.10.20.28.4.61": "PhysicalExamOrder",
   "2.16.840.1.113883.10.20.28.4.130": "Participation",
   "2.16.840.1.113883.10.20.28.4.55": "PatientCharacteristicSex",
@@ -33,7 +38,6 @@
   "2.16.840.1.113883.10.20.28.4.28": "EncounterRecommended",
   "2.16.840.1.113883.10.20.28.4.67": "ProcedurePerformed",
   "2.16.840.1.113883.10.20.28.4.119": "AllergyIntolerance",
-  "2.16.840.1.113883.10.20.28.4.71": "ProviderCharacteristic",
   "22.16.840.1.113883.10.20.28.4.63": "PhysicalExamRecommended",
   "2.16.840.1.113883.10.20.28.4.54": "PatientCharacteristicBirthdate",
   "2.16.840.1.113883.10.20.28.4.120": "AdverseEvent",

data/app/models/model_finder.rb

@@ -6,6 +6,7 @@ module QDM
     def self.by_hqmf_oid(hqmfOid)
       datatype = @hqmfOidToDatatypeMap[hqmfOid]
       return nil if datatype.nil?
+
       return QDM.const_get(datatype)
     end
   end

data/app/models/models.rb

@@ -1,4 +1,4 @@
-# Base QDM module (generated from lib/generate_models.rb) for QDM 5.3
+# Base QDM module (generated from lib/generate_models.rb) for QDM 5.5
 module QDM
 end
 require 'mongoid'
@@ -7,17 +7,25 @@ require 'mongoid'
 require_relative 'model_finder'
 
 # Generated models that are dependencies for base types
-require_relative 'qdm/id'
+require_relative 'qdm/attributes/attribute'
+require_relative 'qdm/attributes/identifier'
 
 # base types
 require_relative 'qdm/basetypes/code'
 require_relative 'qdm/basetypes/data_element'
+require_relative 'qdm/basetypes/date'
 require_relative 'qdm/basetypes/interval'
 require_relative 'qdm/basetypes/quantity'
 require_relative 'qdm/basetypes/ratio'
-require_relative 'qdm/attributes/attribute'
 require_relative 'qdm/attributes/facility_location'
 require_relative 'qdm/attributes/component'
+require_relative 'qdm/attributes/entity'
+require_relative 'qdm/attributes/care_partner'
+require_relative 'qdm/attributes/diagnosis_component'
+require_relative 'qdm/attributes/organization'
+require_relative 'qdm/attributes/patient_entity'
+require_relative 'qdm/attributes/practitioner'
+require_relative 'qdm/attributes/result_component'
 
 # Tacoma-specific models
 require_relative 'cqm/measure'
@@ -38,6 +46,7 @@ require_relative '../../lib/generate_patients'
 
 # Generated models
 require_relative 'qdm/patient'
+require_relative 'qdm/related_person'
 require_relative 'qdm/physical_exam_order'
 require_relative 'qdm/participation'
 require_relative 'qdm/patient_characteristic_sex'
@@ -58,7 +67,6 @@ require_relative 'qdm/device_order'
 require_relative 'qdm/diagnostic_study_performed'
 require_relative 'qdm/intervention_order'
 require_relative 'qdm/family_history'
-require_relative 'qdm/result_component'
 require_relative 'qdm/medication_active'
 require_relative 'qdm/laboratory_test_order'
 require_relative 'qdm/diagnostic_study_order'
@@ -73,7 +81,6 @@ require_relative 'qdm/encounter_order'
 require_relative 'qdm/encounter_recommended'
 require_relative 'qdm/procedure_performed'
 require_relative 'qdm/allergy_intolerance'
-require_relative 'qdm/provider_characteristic'
 require_relative 'qdm/physical_exam_recommended'
 require_relative 'qdm/patient_characteristic_birthdate'
 require_relative 'qdm/adverse_event'