cqm-models 1.0.3 → 1.1.1.0

data/app/assets/javascripts/QDMPatient.js

@@ -0,0 +1,262 @@
+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 AllDataElements = require('./AllDataElements');
+
+const [Schema, Number, String, Mixed] = [
+  mongoose.Schema,
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+  mongoose.Schema.Types.Mixed,
+];
+
+const QDMPatientSchema = new Schema({
+  birthDatetime: DateTime,
+  qdmVersion: { type: String, default: '5.4' },
+
+  // These are the "data criteria", or QDM datatype elements that exist on a
+  // patient.
+  dataElements: [],
+  // This field is for application specific information only. If both Bonnie
+  // Cypress use a common field, it should be made a field on this model,
+  // and not put into extendedData.
+  extendedData: {
+    type: Mixed,
+    default: {},
+  },
+}, { id: false });
+
+// After initialization of a Patient model, initialize every individual data element
+// to its respective Mongoose Model
+QDMPatientSchema.methods.initializeDataElements = function initializeDataElements() {
+  let typeStripped;
+  const dataElementsInit = [];
+  this.dataElements.forEach((element) => {
+    typeStripped = element._type.replace(/QDM::/, '');
+    dataElementsInit.push(new AllDataElements[typeStripped](element));
+  });
+  this.set({ dataElements: dataElementsInit });
+};
+
+QDMPatientSchema.methods.id = function id() {
+  return this._id;
+};
+
+// Returns an array of elements that exist on this patient, that
+// match the given HQMF data criteria OID.
+QDMPatientSchema.methods.getByHqmfOid = function getByHqmfOid(hqmfOid) {
+  return this.dataElements.filter(element => element.hqmfOid === hqmfOid);
+};
+
+// Returns an array of elements that exist on this patient, that
+// match the given QRDA data criteria OID.
+QDMPatientSchema.methods.getByQrdaOid = function getByQrdaOid(qrdaOid) {
+  return this.dataElements.filter(element => element.qrdaOid === qrdaOid);
+};
+
+// Returns an array of elements that exist on this patient. Optionally
+// takes a qdmCategory, which returns all elements of that QDM qdmCategory.
+// Example: patient.getDataElements({qdmCategory: 'encounters'}) will return
+// all Encounter QDM data types active on the patient.
+QDMPatientSchema.methods.getDataElements = function getDataElements(params) {
+  if (params !== undefined && params.qdmCategory !== undefined && params.qdmStatus !== undefined) {
+    return this.dataElements.filter(element => (element.qdmCategory === params.qdmCategory) && (element.qdmStatus === params.qdmStatus));
+  } else if (params !== undefined && params.qdmCategory !== undefined) {
+    return this.dataElements.filter(element => element.qdmCategory === params.qdmCategory);
+  }
+  return this.dataElements;
+};
+
+// 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
+// @param {boolean} isNegated - whether dataElements should be returned based on their negation status
+// @returns {DataElement[]}
+QDMPatientSchema.methods.getByProfile = function getByProfile(profile, isNegated = null) {
+  // If isNegated == true, only return data elements with a negationRationale that is not null.
+  // If isNegated == false, only return data elements with a null negationRationale.
+  // 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) => {
+    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;
+    });
+    return removedMongooseItems;
+  });
+};
+
+// This method is called by the CQL execution engine on a CQLPatient when
+// the execution engine wants information on a record. A record could be patient
+// characteristic information about the patient, or it could be data criteria
+// that currently exist on this patient (data criteria you drag on a patient
+// in Bonnie patient builder).
+// @param {String} profile - the data criteria requested by the execution engine
+// @returns {Object}
+QDMPatientSchema.methods.findRecords = function findRecords(profile) {
+  let profileStripped;
+  if (profile === 'Patient') {
+    // Requested generic patient info
+    const info = { birthDatetime: this.birthDatetime };
+    return [info];
+  } else if (/PatientCharacteristic/.test(profile)) {
+    // Requested a patient characteristic
+    profileStripped = profile.replace(/ *\{[^)]*\} */g, '');
+    return this.getByProfile(profileStripped);
+  } else if (profile != null) {
+    // Requested something else (probably a QDM data type).
+
+    // Strip model details from request. The requested profile string contains
+    // a lot of things we do not need or care about. Example, we might see
+    // something like:
+    // "{urn:healthit-gov:qdm:v5_0_draft}PatientCharacteristicEthnicity"
+    // Where we only care about: "PatientCharacteristicEthnicity".
+    profileStripped = profile.replace(/ *\{[^)]*\} */g, '');
+
+    // Check and handle negation status
+    if (/Positive/.test(profileStripped)) {
+      profileStripped = profileStripped.replace(/Positive/, '');
+      // Since the data criteria is 'Positive', it is not negated.
+      return this.getByProfile(profileStripped, false);
+    } else if (/Negative/.test(profileStripped)) {
+      profileStripped = profileStripped.replace(/Negative/, '');
+      // Since the data criteria is 'Negative', it is negated.
+      return this.getByProfile(profileStripped, true);
+    }
+    // No negation status, proceed normally
+    return this.getByProfile(profileStripped);
+  }
+  return [];
+};
+
+QDMPatientSchema.methods.adverse_events = function adverse_events() {
+  return this.getDataElements({ qdmCategory: 'adverse_event' });
+};
+
+QDMPatientSchema.methods.allergies = function allergies() {
+  return this.getDataElements({ qdmCategory: 'allergy' });
+};
+
+QDMPatientSchema.methods.assessments = function assessments() {
+  return this.getDataElements({ qdmCategory: 'assessment' });
+};
+
+QDMPatientSchema.methods.care_experiences = function care_experiences() {
+  return this.getDataElements({ qdmCategory: 'care_experience' });
+};
+
+QDMPatientSchema.methods.care_goals = function care_goals() {
+  return this.getDataElements({ qdmCategory: 'care_goal' });
+};
+
+QDMPatientSchema.methods.communications = function communications() {
+  return this.getDataElements({ qdmCategory: 'communication' });
+};
+
+QDMPatientSchema.methods.conditions = function conditions() {
+  return this.getDataElements({ qdmCategory: 'condition' });
+};
+
+QDMPatientSchema.methods.devices = function devices() {
+  return this.getDataElements({ qdmCategory: 'device' });
+};
+
+QDMPatientSchema.methods.diagnostic_studies = function diagnostic_studies() {
+  return this.getDataElements({ qdmCategory: 'diagnostic_study' });
+};
+
+QDMPatientSchema.methods.encounters = function encounters() {
+  return this.getDataElements({ qdmCategory: 'encounter' });
+};
+
+QDMPatientSchema.methods.family_history = function family_history() {
+  return this.getDataElements({ qdmCategory: 'family_history' });
+};
+
+QDMPatientSchema.methods.functional_statuses = function functional_statuses() {
+  return this.getDataElements({ qdmCategory: 'functional_status' });
+};
+
+QDMPatientSchema.methods.immunizations = function immunizations() {
+  return this.getDataElements({ qdmCategory: 'immunization' });
+};
+
+QDMPatientSchema.methods.interventions = function interventions() {
+  return this.getDataElements({ qdmCategory: 'intervention' });
+};
+
+QDMPatientSchema.methods.laboratory_tests = function laboratory_tests() {
+  return this.getDataElements({ qdmCategory: 'laboratory_test' });
+};
+
+QDMPatientSchema.methods.medical_equipment = function medical_equipment() {
+  return this.getDataElements({ qdmCategory: 'medical_equipment' });
+};
+
+QDMPatientSchema.methods.medications = function medications() {
+  return this.getDataElements({ qdmCategory: 'medication' });
+};
+
+QDMPatientSchema.methods.patient_characteristics = function patient_characteristics() {
+  return this.getDataElements({ qdmCategory: 'patient_characteristic' });
+};
+
+QDMPatientSchema.methods.physical_exams = function physical_exams() {
+  return this.getDataElements({ qdmCategory: 'physical_exam' });
+};
+
+QDMPatientSchema.methods.preferences = function preferences() {
+  return this.getDataElements({ qdmCategory: 'preference' });
+};
+
+QDMPatientSchema.methods.provider_characteristics = function provider_characteristics() {
+  return this.getDataElements({ qdmCategory: 'provider_characteristic' });
+};
+
+QDMPatientSchema.methods.procedures = function procedures() {
+  return this.getDataElements({ qdmCategory: 'procedure' });
+};
+
+QDMPatientSchema.methods.results = function results() {
+  return this.getDataElements({ qdmCategory: 'result' });
+};
+
+QDMPatientSchema.methods.risk_category_assessments = function risk_category_assessments() {
+  return this.getDataElements({ qdmCategory: 'risk_category_assessment' });
+};
+
+QDMPatientSchema.methods.social_history = function social_history() {
+  return this.getDataElements({ qdmCategory: 'social_history' });
+};
+
+QDMPatientSchema.methods.substances = function substances() {
+  return this.getDataElements({ qdmCategory: 'substance' });
+};
+
+QDMPatientSchema.methods.symptoms = function symptoms() {
+  return this.getDataElements({ qdmCategory: 'symptom' });
+};
+
+QDMPatientSchema.methods.system_characteristics = function system_characteristics() {
+  return this.getDataElements({ qdmCategory: 'system_characteristic' });
+};
+
+QDMPatientSchema.methods.transfers = function transfers() {
+  return this.getDataElements({ qdmCategory: 'transfer' });
+};
+
+QDMPatientSchema.methods.vital_signs = function vital_signs() {
+  return this.getDataElements({ qdmCategory: 'vital_sign' });
+};
+
+module.exports.QDMPatientSchema = QDMPatientSchema;
+class QDMPatient extends mongoose.Document {
+  constructor(object) {
+    super(object, QDMPatientSchema);
+    this.initializeDataElements();
+  }
+}
+module.exports.QDMPatient = QDMPatient;

data/app/assets/javascripts/Result.js

@@ -1,4 +1,4 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
 
 const PlaceholderResultSchema = mongoose.Schema({
   cache_id: String,
@@ -25,4 +25,9 @@ const PlaceholderResultSchema = mongoose.Schema({
 });
 
 module.exports.ResultSchema = PlaceholderResultSchema;
-module.exports.Result = mongoose.model('Result', PlaceholderResultSchema);
+class PlaceholderResult extends mongoose.Document {
+  constructor(object) {
+    super(object, PlaceholderResultSchema);
+  }
+}
+module.exports.PlaceholderResult = PlaceholderResult;

data/app/assets/javascripts/ResultComponent.js

@@ -1,13 +1,15 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
+
+const { IdSchema } = require('./Id');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
-
-const { FacilityLocationSchema } = require('./FacilityLocation');
-const { IdSchema } = require('./Id');
 const Any = require('./basetypes/Any');
+const { ComponentSchema } = require('./attributes/Component');
+const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+
 
 const [Number, String] = [
   mongoose.Schema.Types.Number,
@@ -17,9 +19,15 @@ const [Number, String] = [
 const ResultComponentSchema = DataElementSchema({
   referenceRange: Interval,
   qdmVersion: { type: String, default: '5.4' },
-  _type: { type: String, default: 'ResultComponent' },
+  _type: { type: String, default: 'QDM::ResultComponent' },
 
 });
 
 module.exports.ResultComponentSchema = ResultComponentSchema;
-module.exports.ResultComponent = mongoose.model('ResultComponent', ResultComponentSchema);
+class ResultComponent extends mongoose.Document {
+  constructor(object) {
+    super(object, ResultComponentSchema);
+    this._type = 'QDM::ResultComponent';
+  }
+}
+module.exports.ResultComponent = ResultComponent;

data/app/assets/javascripts/SubstanceAdministered.js

@@ -1,13 +1,15 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
+
+const { IdSchema } = require('./Id');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
-const { ComponentSchema } = require('./Component');
-const { FacilityLocationSchema } = require('./FacilityLocation');
-const { IdSchema } = require('./Id');
 const Any = require('./basetypes/Any');
+const { ComponentSchema } = require('./attributes/Component');
+const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+
 
 const [Number, String] = [
   mongoose.Schema.Types.Number,
@@ -21,13 +23,20 @@ const SubstanceAdministeredSchema = DataElementSchema({
   frequency: Code,
   route: Code,
   negationRationale: Code,
-  hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.3.73' },
+  qdmTitle: { type: String, default: 'Substance, Administered' },
+  hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.73' },
   qdmCategory: { type: String, default: 'substance' },
   qdmStatus: { type: String, default: 'administered' },
   qdmVersion: { type: String, default: '5.4' },
-  _type: { type: String, default: 'SubstanceAdministered' },
+  _type: { type: String, default: 'QDM::SubstanceAdministered' },
 
 });
 
 module.exports.SubstanceAdministeredSchema = SubstanceAdministeredSchema;
-module.exports.SubstanceAdministered = mongoose.model('SubstanceAdministered', SubstanceAdministeredSchema);
+class SubstanceAdministered extends mongoose.Document {
+  constructor(object) {
+    super(object, SubstanceAdministeredSchema);
+    this._type = 'QDM::SubstanceAdministered';
+  }
+}
+module.exports.SubstanceAdministered = SubstanceAdministered;

data/app/assets/javascripts/SubstanceOrder.js

@@ -1,13 +1,15 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
+
+const { IdSchema } = require('./Id');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
-const { ComponentSchema } = require('./Component');
-const { FacilityLocationSchema } = require('./FacilityLocation');
-const { IdSchema } = require('./Id');
 const Any = require('./basetypes/Any');
+const { ComponentSchema } = require('./attributes/Component');
+const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+
 
 const [Number, String] = [
   mongoose.Schema.Types.Number,
@@ -23,13 +25,20 @@ const SubstanceOrderSchema = DataElementSchema({
   refills: Number,
   route: Code,
   negationRationale: Code,
-  hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.3.77' },
+  qdmTitle: { type: String, default: 'Substance, Order' },
+  hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.77' },
   qdmCategory: { type: String, default: 'substance' },
   qdmStatus: { type: String, default: 'order' },
   qdmVersion: { type: String, default: '5.4' },
-  _type: { type: String, default: 'SubstanceOrder' },
+  _type: { type: String, default: 'QDM::SubstanceOrder' },
 
 });
 
 module.exports.SubstanceOrderSchema = SubstanceOrderSchema;
-module.exports.SubstanceOrder = mongoose.model('SubstanceOrder', SubstanceOrderSchema);
+class SubstanceOrder extends mongoose.Document {
+  constructor(object) {
+    super(object, SubstanceOrderSchema);
+    this._type = 'QDM::SubstanceOrder';
+  }
+}
+module.exports.SubstanceOrder = SubstanceOrder;

data/app/assets/javascripts/SubstanceRecommended.js

@@ -1,13 +1,15 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
+
+const { IdSchema } = require('./Id');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
-const { ComponentSchema } = require('./Component');
-const { FacilityLocationSchema } = require('./FacilityLocation');
-const { IdSchema } = require('./Id');
 const Any = require('./basetypes/Any');
+const { ComponentSchema } = require('./attributes/Component');
+const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+
 
 const [Number, String] = [
   mongoose.Schema.Types.Number,
@@ -22,13 +24,20 @@ const SubstanceRecommendedSchema = DataElementSchema({
   refills: Number,
   route: Code,
   negationRationale: Code,
-  hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.3.78' },
+  qdmTitle: { type: String, default: 'Substance, Recommended' },
+  hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.78' },
   qdmCategory: { type: String, default: 'substance' },
   qdmStatus: { type: String, default: 'recommended' },
   qdmVersion: { type: String, default: '5.4' },
-  _type: { type: String, default: 'SubstanceRecommended' },
+  _type: { type: String, default: 'QDM::SubstanceRecommended' },
 
 });
 
 module.exports.SubstanceRecommendedSchema = SubstanceRecommendedSchema;
-module.exports.SubstanceRecommended = mongoose.model('SubstanceRecommended', SubstanceRecommendedSchema);
+class SubstanceRecommended extends mongoose.Document {
+  constructor(object) {
+    super(object, SubstanceRecommendedSchema);
+    this._type = 'QDM::SubstanceRecommended';
+  }
+}
+module.exports.SubstanceRecommended = SubstanceRecommended;

data/app/assets/javascripts/Symptom.js

@@ -1,13 +1,15 @@
-const mongoose = require('mongoose');
+const mongoose = require('mongoose/browser');
+
+const { IdSchema } = require('./Id');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
-const { ComponentSchema } = require('./Component');
-const { FacilityLocationSchema } = require('./FacilityLocation');
-const { IdSchema } = require('./Id');
 const Any = require('./basetypes/Any');
+const { ComponentSchema } = require('./attributes/Component');
+const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+
 
 const [Number, String] = [
   mongoose.Schema.Types.Number,
@@ -17,13 +19,20 @@ const [Number, String] = [
 const SymptomSchema = DataElementSchema({
   prevalencePeriod: Interval,
   severity: Code,
-  hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.3.116' },
+  qdmTitle: { type: String, default: 'Symptom' },
+  hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.116' },
   qrdaOid: { type: String, default: '2.16.840.1.113883.10.20.24.3.136' },
   qdmCategory: { type: String, default: 'symptom' },
   qdmVersion: { type: String, default: '5.4' },
-  _type: { type: String, default: 'Symptom' },
+  _type: { type: String, default: 'QDM::Symptom' },
 
 });
 
 module.exports.SymptomSchema = SymptomSchema;
-module.exports.Symptom = mongoose.model('Symptom', SymptomSchema);
+class Symptom extends mongoose.Document {
+  constructor(object) {
+    super(object, SymptomSchema);
+    this._type = 'QDM::Symptom';
+  }
+}
+module.exports.Symptom = Symptom;