cqm-models 0.7.2

data/templates/index_template.js.erb

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+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;

data/templates/models_template.rb.erb

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+# Base QDM module (generated from lib/generate_models.rb) for QDM 5.3
+module QDM
+end
+require 'mongoid'
+
+# base types
+require_relative 'qdm/basetypes/code'
+require_relative 'qdm/basetypes/interval'
+require_relative 'qdm/basetypes/quantity'
+require_relative 'qdm/basetypes/data_element'
+
+# Tacoma-specific models
+require_relative 'qdm/tacoma/measure'
+require_relative 'qdm/tacoma/measure_package'
+require_relative 'qdm/tacoma/valueset'
+require_relative 'qdm/tacoma/concept'
+
+# Generated models
+<%- datatypes.each_key do |datatype| -%>
+require_relative 'qdm/<%= datatype.underscore %>'
+<%- end -%>

data/templates/mongoose_template.js.erb

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+const mongoose = require('mongoose');
+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 [Number, String] = [
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+];
+
+const <%= datatype -%>Schema = DataElementSchema({
+  <%- for attribute in attrs_with_extras -%>
+  <%= attribute[:name] %>: <%= TYPE_LOOKUP_JS[attribute[:type]] -%>,
+  <%- end %>
+});
+
+module.exports.<%= datatype %>Schema = <%= datatype %>Schema;
+module.exports.<%= datatype %> = mongoose.model('<%= datatype %>', <%= datatype %>Schema);

data/templates/patient_extension.rb.erb

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+  field :givenNames, type: Array
+  field :familyName, type: String
+  field :bundleId, type: String
+
+  # These are the "data criteria", or QDM datatype elements that exist on a
+  # patient.
+  embeds_many :dataElements, class_name: 'QDM::DataElement'
+
+  # 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.
+  field :extendedData, type: Hash
+
+  # Returns an array of elements that exist on this patient, that
+  # match the given HQMF data criteria OID.
+  def get_by_hqmf_oid(hqmf_oid)
+    dataElements.where(hqmfOid: hqmf_oid) || []
+  end
+
+  # Returns an array of elements that exist on this patient, that
+  # match the given QRDA data criteria OID.
+  def get_by_qrda_oid(qrda_oid)
+    dataElements.where(qrdaOid: qrda_oid) || []
+  end
+
+  # Returns an array of elements that exist on this patient. Optionally
+  # takes a category and/or, which returns all elements of that QDM
+  # category. Example: patient.get_data_elements('encounters')
+  # will return all Encounter QDM data types active on the patient.
+  def get_data_elements(category = nil, status = nil)
+    if category && status
+      dataElements.where(category: category, qdmStatus: status) || []
+    elsif category
+      dataElements.where(category: category) || []
+    else
+      dataElements || []
+    end
+  end
+
+  # Helper method; returns adverse_event data element types on this patient.
+  def adverse_events
+    get_data_elements('adverse_event')
+  end
+
+  # Helper method; returns allergy data element types on this patient.
+  def allergies
+    get_data_elements('allergy')
+  end
+
+  # Helper method; returns assessment data element types on this patient.
+  def assessments
+    get_data_elements('assessment')
+  end
+
+  # Helper method; returns care_experience data element types on this patient.
+  def care_experiences
+    get_data_elements('care_experience')
+  end
+
+  # Helper method; returns care_goal data element types on this patient.
+  def care_goals
+    get_data_elements('care_goal')
+  end
+
+  # Helper method; returns communication data element types on this patient.
+  def communications
+    get_data_elements('communication')
+  end
+
+  # Helper method; returns condition data element types on this patient.
+  def conditions
+    get_data_elements('condition')
+  end
+
+  # Helper method; returns device data element types on this patient.
+  def devices
+    get_data_elements('device')
+  end
+
+  # Helper method; returns diagnostic_study data element types on this patient.
+  def diagnostic_studies
+    get_data_elements('diagnostic_study')
+  end
+
+  # Helper method; returns encounter data element types on this patient.
+  def encounters
+    get_data_elements('encounter')
+  end
+
+  # Helper method; returns family_history data element types on this patient.
+  def family_history
+    get_data_elements('family_history')
+  end
+
+  # Helper method; returns functional_status data element types on this patient.
+  def functional_statuses
+    get_data_elements('functional_status')
+  end
+
+  # Helper method; returns immunization data element types on this patient.
+  def immunizations
+    get_data_elements('immunization')
+  end
+
+  # Helper method; returns intervention data element types on this patient.
+  def interventions
+    get_data_elements('intervention')
+  end
+
+  # Helper method; returns laboratory_test data element types on this patient.
+  def laboratory_tests
+    get_data_elements('laboratory_test')
+  end
+
+  # Helper method; returns medical_equipment data element types on this patient.
+  def medical_equipment
+    get_data_elements('medical_equipment')
+  end
+
+  # Helper method; returns medication data element types on this patient.
+  def medications
+    get_data_elements('medication')
+  end
+
+  # Helper method; returns physical_exam data element types on this patient.
+  def physical_exams
+    get_data_elements('physical_exam')
+  end
+
+  # Helper method; returns preference data element types on this patient.
+  def preferences
+    get_data_elements('preference')
+  end
+
+  # Helper method; returns provider_characteristic data element types on this patient.
+  def provider_characteristics
+    get_data_elements('provider_characteristic')
+  end
+
+  # Helper method; returns procedure data element types on this patient.
+  def procedures
+    get_data_elements('procedure')
+  end
+
+  # Helper method; returns result data element types on this patient.
+  def results
+    get_data_elements('result')
+  end
+
+  # Helper method; returns risk_category_assessment data element types on this patient.
+  def risk_category_assessments
+    get_data_elements('risk_category_assessment')
+  end
+
+  # Helper method; returns social_history data element types on this patient.
+  def social_history
+    get_data_elements('social_history')
+  end
+
+  # Helper method; returns substance data element types on this patient.
+  def substances
+    get_data_elements('substance')
+  end
+
+  # Helper method; returns symptom data element types on this patient.
+  def symptoms
+    get_data_elements('symptom')
+  end
+
+  # Helper method; returns system_characteristic data element types on this patient.
+  def system_characteristics
+    get_data_elements('system_characteristic')
+  end
+
+  # Helper method; returns transfer data element types on this patient.
+  def transfers
+    get_data_elements('transfer')
+  end
+
+  # Helper method; returns vital_sign data element types on this patient.
+  def vital_signs
+    get_data_elements('vital_sign')
+  end
+
+  # Return the Mongo id.
+  def id
+    _id
+  end
+
+  # Include '_type' in any JSON output. This is necessary for deserialization.
+  def to_json(options = nil)
+    serializable_hash(methods: :_type).to_json(options)
+  end
+end

data/templates/patient_template.js.erb

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+const mongoose = require('mongoose');
+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] = [
+  mongoose.Schema,
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+];
+
+const PatientSchema = new Schema({
+  <%- for attribute in attrs_with_extras -%>
+  <%= attribute[:name] %>: <%= TYPE_LOOKUP_JS[attribute[:type]] -%>,
+  <%- end %>
+  givenNames: [String],
+  familyName: String,
+  bundleId: String,
+  // 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: {},
+}, { id: false });
+
+// After initialization of a Patient model, initialize every individual data element
+// to its respective Mongoose Model
+PatientSchema.methods.initializeDataElements = function initializeDataElements() {
+  let typeStripped;
+  const dataElementsInit = [];
+  this.dataElements.forEach((element) => {
+    typeStripped = element._type.replace(/QDM::/, '');
+    if (typeStripped in AllDataElements) {
+      dataElementsInit.push(AllDataElements[typeStripped](element));
+    } else {
+      dataElementsInit.push(element);
+    }
+  });
+  this.set({ dataElements: dataElementsInit });
+};
+
+PatientSchema.queue('initializeDataElements');
+
+PatientSchema.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.
+PatientSchema.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.
+PatientSchema.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 category, which returns all elements of that QDM category.
+// Example: patient.getDataElements(category = 'encounters') will return
+// all Encounter QDM data types active on the patient.
+PatientSchema.methods.getDataElements = function getDataElements(params) {
+  if (params.category && params.qdmStatus) {
+    return this.dataElements.filter(element => (element.category === params.category) && (element.qdmStatus === params.qdmStatus));
+  } else if (params.category) {
+    return this.dataElements.filter(element => element.category === params.category);
+  }
+  return this.dataElements;
+};
+
+// Returns an array of dataElements that exist on the patient, queried by
+// QDM profile
+PatientSchema.methods.getByProfile = function getByProfile(profile, isNegated = null) {
+  if (isNegated === true) {
+    return this.dataElements.filter(element => element._type === `QDM::${profile}` && (typeof element.negationRationale !== 'undefined' && element.negationRationale != null));
+  } else if (isNegated === false) {
+    return this.dataElements.filter(element => element._type === `QDM::${profile}` && (typeof element.negationRationale === 'undefined' || element.negationRationale == null));
+  }
+  return this.dataElements.filter(element => element._type === `QDM::${profile}`);
+};
+
+// 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's patient builder).
+// @param {String} profile - the data criteria requested by the execution engine
+// @returns {Object}
+PatientSchema.methods.findRecords = function findRecords(profile) {
+  let profileStripped;
+  if (profile === 'Patient') {
+    // Requested generic patient info
+    return { birthDatetime: this.birthDatetime };
+  } 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 don't 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 [];
+};
+
+PatientSchema.methods.adverse_events = function adverse_events() {
+  return this.getDataElements({ category: 'adverse_event' });
+};
+
+PatientSchema.methods.allergies = function allergies() {
+  return this.getDataElements({ category: 'allergy' });
+};
+
+PatientSchema.methods.assessments = function assessments() {
+  return this.getDataElements({ category: 'assessment' });
+};
+
+PatientSchema.methods.care_experiences = function care_experiences() {
+  return this.getDataElements({ category: 'care_experience' });
+};
+
+PatientSchema.methods.care_goals = function care_goals() {
+  return this.getDataElements({ category: 'care_goal' });
+};
+
+PatientSchema.methods.communications = function communications() {
+  return this.getDataElements({ category: 'communication' });
+};
+
+PatientSchema.methods.conditions = function conditions() {
+  return this.getDataElements({ category: 'condition' });
+};
+
+PatientSchema.methods.devices = function devices() {
+  return this.getDataElements({ category: 'device' });
+};
+
+PatientSchema.methods.diagnostic_studies = function diagnostic_studies() {
+  return this.getDataElements({ category: 'diagnostic_study' });
+};
+
+PatientSchema.methods.encounters = function encounters() {
+  return this.getDataElements({ category: 'encounter' });
+};
+
+PatientSchema.methods.family_history = function family_history() {
+  return this.getDataElements({ category: 'family_history' });
+};
+
+PatientSchema.methods.functional_statuses = function functional_statuses() {
+  return this.getDataElements({ category: 'functional_status' });
+};
+
+PatientSchema.methods.immunizations = function immunizations() {
+  return this.getDataElements({ category: 'immunization' });
+};
+
+PatientSchema.methods.interventions = function interventions() {
+  return this.getDataElements({ category: 'intervention' });
+};
+
+PatientSchema.methods.laboratory_tests = function laboratory_tests() {
+  return this.getDataElements({ category: 'laboratory_test' });
+};
+
+PatientSchema.methods.medical_equipment = function medical_equipment() {
+  return this.getDataElements({ category: 'medical_equipment' });
+};
+
+PatientSchema.methods.medications = function medications() {
+  return this.getDataElements({ category: 'medication' });
+};
+
+PatientSchema.methods.physical_exams = function physical_exams() {
+  return this.getDataElements({ category: 'physical_exam' });
+};
+
+PatientSchema.methods.preferences = function preferences() {
+  return this.getDataElements({ category: 'preference' });
+};
+
+PatientSchema.methods.provider_characteristics = function provider_characteristics() {
+  return this.getDataElements({ category: 'provider_characteristic' });
+};
+
+PatientSchema.methods.procedures = function procedures() {
+  return this.getDataElements({ category: 'procedure' });
+};
+
+PatientSchema.methods.results = function results() {
+  return this.getDataElements({ category: 'result' });
+};
+
+PatientSchema.methods.risk_category_assessments = function risk_category_assessments() {
+  return this.getDataElements({ category: 'risk_category_assessment' });
+};
+
+PatientSchema.methods.social_history = function social_history() {
+  return this.getDataElements({ category: 'social_history' });
+};
+
+PatientSchema.methods.substances = function substances() {
+  return this.getDataElements({ category: 'substance' });
+};
+
+PatientSchema.methods.symptoms = function symptoms() {
+  return this.getDataElements({ category: 'symptom' });
+};
+
+PatientSchema.methods.system_characteristics = function system_characteristics() {
+  return this.getDataElements({ category: 'system_characteristic' });
+};
+
+PatientSchema.methods.transfers = function transfers() {
+  return this.getDataElements({ category: 'transfer' });
+};
+
+PatientSchema.methods.vital_signs = function vital_signs() {
+  return this.getDataElements({ category: 'vital_sign' });
+};
+
+module.exports.PatientSchema = PatientSchema;
+module.exports.Patient = mongoose.model('Patient', PatientSchema);