cqm-models 0.8.0 → 0.8.1

data/lib/generate_models.rb

@@ -284,6 +284,12 @@ files = Dir.glob(js_models_path + '*.js').each do |file_name|
   # Add class
   contents.gsub!(/  _type: String,\n/, "  _type: { type: String, default: '#{dc_name.camelize}' },\n")
 
+  # Component and Facility types
+  contents.gsub!(/facilityLocations: \[\]/, 'facilityLocations: [FacilityLocationSchema]')
+  contents.gsub!(/facilityLocation: Code/, 'facilityLocation: FacilityLocationSchema')
+  contents.gsub!(/components: \[\]/, 'components: [ComponentSchema]')
+  contents.gsub!(/component: Code/, 'component: ComponentSchema')
+
   File.open(file_name, 'w') { |file| file.puts contents }
 end
 

data/package.json

@@ -1,13 +1,13 @@
 {
   "name": "cqm-models",
-  "version": "0.8.0",
+  "version": "0.8.1",
   "description": "This library contains auto generated Mongo (Mongoose.js) models that correspond to the QDM (Quality Data Model) specification.",
   "main": "app/assets/javascripts/index.js",
   "browser": {
     "index.js": "dist/index.js"
   },
   "repository": "https://github.com/projecttacoma/cqm-models.git",
-  "homepage": "https://github.com/projectcypress/cqm-models#readme",
+  "homepage": "https://github.com/projecttacoma/cqm-models#readme",
   "contributors": [
     "Louis Ades <lades@mitre.org>",
     "Michael O'Keefe <mokeefe@mitre.org>",
@@ -15,7 +15,7 @@
   ],
   "license": "Apache-2.0",
   "dependencies": {
-    "cql-execution": "1.2.1",
+    "cql-execution": "1.2.2",
     "mongoose": "^5.0.7"
   },
   "devDependencies": {

data/templates/models_template.rb.erb

@@ -14,6 +14,7 @@ require_relative 'qdm/tacoma/measure'
 require_relative 'qdm/tacoma/measure_package'
 require_relative 'qdm/tacoma/valueset'
 require_relative 'qdm/tacoma/concept'
+require_relative 'qdm/tacoma/individual_result'
 
 # Generated models
 <%- datatypes.each_key do |datatype| -%>

data/templates/mongoose_template.js.erb

@@ -4,18 +4,26 @@ const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+<% unless datatype.downcase.include? 'component' %>const { ComponentSchema } = require('./Component');<% end %>
+<% unless datatype.downcase.include? 'facilitylocation' %>const { FacilityLocationSchema } = require('./FacilityLocation');<% end %>
 const Any = require('./basetypes/Any');
 
 const [Number, String] = [
   mongoose.Schema.Types.Number,
   mongoose.Schema.Types.String,
 ];
-
+<% unless datatype == 'Component' || datatype == 'FacilityLocation' %>
 const <%= datatype -%>Schema = DataElementSchema({
   <%- for attribute in attrs_with_extras -%>
   <%= attribute[:name] %>: <%= TYPE_LOOKUP_JS[attribute[:type]] -%>,
   <%- end %>
 });
-
+<% else %>
+const <%= datatype -%>Schema = new mongoose.Schema({
+  <%- for attribute in attrs_with_extras -%>
+  <%= attribute[:name] %>: <%= TYPE_LOOKUP_JS[attribute[:type]] -%>,
+  <%- end %>
+});
+<% end %>
 module.exports.<%= datatype %>Schema = <%= datatype %>Schema;
 module.exports.<%= datatype %> = mongoose.model('<%= datatype %>', <%= datatype %>Schema);

data/templates/patient_extension.rb.erb

@@ -23,6 +23,17 @@
     dataElements.where(qrdaOid: qrda_oid) || []
   end
 
+  # Shift all data element fields that deal with dates by the given value.
+  # Given value should be in seconds. Positive values shift forward, negative
+  # values shift backwards.
+  #
+  # Note: This will shift dates of the birthdate and
+  # dates on the data elements that exist on the patient.
+  def shift_dates(seconds)
+    self.birthDatetime = (birthDatetime.utc.to_time + seconds.seconds).to_datetime
+    dataElements.each { |element| element.shift_dates(seconds) }
+  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')
@@ -191,4 +202,4 @@
   def to_json(options = nil)
     serializable_hash(methods: :_type).to_json(options)
   end
-end
+end

data/templates/patient_template.js.erb

@@ -5,10 +5,11 @@ const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
 const AllDataElements = require('./AllDataElements');
 
-const [Schema, Number, String] = [
+const [Schema, Number, String, Mixed] = [
   mongoose.Schema,
   mongoose.Schema.Types.Number,
   mongoose.Schema.Types.String,
+  mongoose.Schema.Types.Mixed,
 ];
 
 const PatientSchema = new Schema({
@@ -24,7 +25,10 @@ const PatientSchema = new Schema({
   // 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: {},
+  extendedData: {
+    type: Mixed,
+    default: {},
+  },
 }, { id: false });
 
 // After initialization of a Patient model, initialize every individual data element
@@ -77,26 +81,35 @@ PatientSchema.methods.getDataElements = function getDataElements(params) {
 // 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::${profile}`);
+  // If isNegated == true, only return data elements with a negationRationale that is not null.
+  // If isNegated == false, only return data elements with a null negationRationale.
+  // If isNegated == null, return all matching data elements by type, regardless of negationRationale.
+  const results = this.dataElements.filter(element => element._type === `QDM::${profile}` && (isNegated === null || !!element.negationRationale === isNegated));
+  return results.map((result) => {
+    const getCodeFunction = Object.getPrototypeOf(result).getCode;
+    const codeFunction = Object.getPrototypeOf(result).code;
+    const removedMongooseItems = AllDataElements[profile](result).toObject();
+    // toObject() will remove all mongoose functions but also removed the getCode and code functions
+    // the execution engine requires the code and getCode functions so we have to add them back
+    removedMongooseItems.getCode = getCodeFunction;
+    removedMongooseItems.code = codeFunction;
+    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's patient builder).
+// in Bonnie 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 };
+    const info = { birthDatetime: this.birthDatetime };
+    return [info];
   } else if (/PatientCharacteristic/.test(profile)) {
     // Requested a patient characteristic
     profileStripped = profile.replace(/ *\{[^)]*\} */g, '');
@@ -105,7 +118,7 @@ PatientSchema.methods.findRecords = function findRecords(profile) {
     // 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
+    // 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".

data/yarn.lock

@@ -442,9 +442,9 @@ core-util-is@~1.0.0:
   version "1.0.2"
   resolved "https://registry.yarnpkg.com/core-util-is/-/core-util-is-1.0.2.tgz#b5fd54220aa2bc5ab57aab7140c940754503c1a7"
 
-cql-execution@1.2.1:
-  version "1.2.1"
-  resolved "https://registry.yarnpkg.com/cql-execution/-/cql-execution-1.2.1.tgz#9dbf19a7da400ee4236c4f5037b927c884a1fb46"
+cql-execution@1.2.2:
+  version "1.2.2"
+  resolved "https://registry.yarnpkg.com/cql-execution/-/cql-execution-1.2.2.tgz#2d8933e96edc2c0ff04992444fc8d79e3cb556bb"
   dependencies:
     moment "^2.20.1"
     ucum "0.0.7"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cqm-models
 version: !ruby/object:Gem::Version
-  version: 0.8.0
+  version: 0.8.1
 platform: ruby
 authors:
 - aholmes@mitre.org
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2018-07-02 00:00:00.000000000 Z
+date: 2018-07-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -316,7 +316,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.11
+rubygems_version: 2.6.12
 signing_key: 
 specification_version: 4
 summary: Mongo models that correspond to the QDM specification.