cqm-models 0.7.7 → 0.8.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rubocop.yml

@@ -37,6 +37,9 @@ Naming/UncommunicativeMethodParamName:
 Naming/VariableName:
   Enabled: false
 
+Style/DateTime:
+  Enabled: false
+
 # Only disabled until the cyclomatic complexity method in measure.rb (ported from bonnie-bundler) is rewritten
 Lint/NestedMethodDefinition:
   Enabled: false

data/README.md

@@ -1,5 +1,6 @@
 [![Build Status](https://travis-ci.org/projecttacoma/cqm-models.svg?branch=master)](https://travis-ci.org/projecttacoma/cqm-models)
 [![Gem Version](https://badge.fury.io/rb/cqm-models.svg)](https://badge.fury.io/rb/cqm-models)
+![NPM](https://img.shields.io/npm/v/cqm-models.svg)
 
 # cqm-models
 

data/app/assets/javascripts/IndividualResult.js

@@ -0,0 +1,54 @@
+const mongoose = require('mongoose');
+
+const [Number, String, Mixed, ObjectId] = [
+  mongoose.Schema.Types.Number,
+  mongoose.Schema.Types.String,
+  mongoose.Schema.Types.Mixed,
+  mongoose.Schema.Types.ObjectId,
+];
+
+const IndividualResultSchema = mongoose.Schema(
+  {
+    // Population Attributes
+    STRAT: Number,
+    IPP: Number,
+    DENOM: Number,
+    NUMER: Number,
+    NUMEX: Number,
+    DENEX: Number,
+    DENEXCEP: Number,
+    MSRPOPL: Number,
+    OBSERV: Number,
+    MSRPOPLEX: Number,
+
+    // Result Attributes
+    clause_results: Mixed,
+    episode_results: Mixed,
+    statement_results: Mixed,
+
+    // This field is for application specific information only. If both Bonnie and
+    // Cypress use a common field, it should be made a field on this model,
+    // and not put into extendedData.
+    extendedData: {},
+
+    // Calculation State attributes
+    state: {
+      type: String,
+      enum: ['queued', 'running', 'complete', 'cancelled', 'failed'],
+      default: 'queued',
+    },
+
+    // Relations to other model classes
+    // 'alias' field makes it so you can call obj.measure, and get the object referenced by measure_id
+    measure_id: { type: ObjectId, ref: 'Measure', alias: 'measure' },
+    patient_id: { type: ObjectId, ref: 'Patient', alias: 'patient' },
+
+  },
+  // Options
+  {
+    timestamps: { createdAt: 'created_at', updatedAt: 'updated_at' }, // These are the Mongoid conventions for timestamps
+  }
+);
+
+module.exports.IndividualResultSchema = IndividualResultSchema;
+module.exports.IndividualResult = mongoose.model('individual_result', IndividualResultSchema);

data/app/assets/javascripts/Measure.js

@@ -3,7 +3,7 @@ const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 
-const [mNumber, mString, mBoolean, Mixed, ObjectId, mDate] = [
+const [Number, String, Boolean, Mixed, ObjectId, Date] = [
   mongoose.Schema.Types.Number,
   mongoose.Schema.Types.String,
   mongoose.Schema.Types.Boolean,
@@ -15,32 +15,32 @@ const [mNumber, mString, mBoolean, Mixed, ObjectId, mDate] = [
 const MeasureSchema = mongoose.Schema(
   {
     // ID/other measure information
-    id: mString,
-    measure_id: mString,
-    hqmf_id: mString,
-    hqmf_set_id: mString,
-    hqmf_version_number: mNumber,
-    cms_id: mString,
-    title: mString,
-    description: mString,
-    type: mString,
-    category: { type: mString, default: 'Uncategorized' },
+    id: String,
+    measure_id: String,
+    hqmf_id: String,
+    hqmf_set_id: String,
+    hqmf_version_number: Number,
+    cms_id: String,
+    title: String,
+    description: String,
+    type: String,
+    category: { type: String, default: 'Uncategorized' },
 
     // Measure type variables
-    episode_of_care: mBoolean,
-    continuous_constiable: mBoolean,
+    episode_of_care: Boolean,
+    continuous_constiable: Boolean,
     episode_ids: [],
 
     // Publishing data (used by Bonnie)
-    published: mBoolean,
-    publish_date: mDate,
-    version: mNumber,
+    published: Boolean,
+    publish_date: Date,
+    version: Number,
 
     // ELM/CQL Measure-logic related data
     elm_annotations: Mixed,
-    cql: [mString],
+    cql: [String],
     elm: [Mixed],
-    main_cql_library: mString,
+    main_cql_library: String,
     cql_statement_dependencies: Mixed,
 
     // HQMF/Tacoma-specific Measure-logic related data

data/app/assets/javascripts/Patient.js

@@ -97,7 +97,8 @@ 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, '');

data/app/assets/javascripts/ValueSet.js

@@ -1,7 +1,7 @@
 const mongoose = require('mongoose');
 const Concept = require('./Concept.js');
 
-const [mString, Mixed, ObjectId] = [
+const [String, Mixed, ObjectId] = [
   mongoose.Schema.Types.String,
   mongoose.Schema.Types.Mixed,
   mongoose.Schema.Types.ObjectId,
@@ -9,9 +9,9 @@ const [mString, Mixed, ObjectId] = [
 
 const ValueSetSchema = mongoose.Schema(
   {
-    oid: mString,
-    display_name: mString,
-    version: mString,
+    oid: String,
+    display_name: String,
+    version: String,
     categories: Mixed,
 
     concepts: [Concept.ConceptSchema],

data/app/assets/javascripts/index.js

@@ -10,3 +10,5 @@ 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.IndividualResult = require('./IndividualResult').IndividualResult;
+module.exports.IndividualResultSchema = require('./IndividualResult').IndividualResultSchema;

data/app/models/models.rb

@@ -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
 require_relative 'qdm/patient'

data/app/models/qdm/basetypes/data_element.rb

@@ -47,6 +47,23 @@ module QDM
       serializable_hash(methods: :_type).to_json(options)
     end
 
+    # Shift all fields that deal with dates by the given value.
+    # Given value should be in seconds. Positive values shift forward, negative
+    # values shift backwards.
+    def shift_dates(seconds)
+      # Iterate over fields
+      fields.keys.each do |field|
+        # Check if field is a DateTime
+        if send(field).is_a? DateTime
+          send(field + '=', (send(field).to_time + seconds.seconds).to_datetime)
+        end
+        # Check if field is an Interval
+        if (send(field).is_a? Interval) || (send(field).is_a? DataElement)
+          send(field + '=', send(field).shift_dates(seconds))
+        end
+      end
+    end
+
     class << self
       # Get the object as it was stored in the database, and instantiate
       # this custom class from it.

data/app/models/qdm/basetypes/interval.rb

@@ -16,6 +16,21 @@ module QDM
       { low: @low, high: @high, lowClosed: @lowClosed, highClosed: @highClosed, _type: 'QDM::Interval' }
     end
 
+    # Shift dates by the given value.
+    # Given value should be in seconds. Positive values shift forward, negative
+    # values shift backwards.
+    #
+    # NOTE: This will only shift if @high and @low are DateTimes.
+    def shift_dates(seconds)
+      if (@low.is_a? DateTime) || (@low.is_a? Time)
+        @low = (@low.utc.to_time + seconds.seconds).to_datetime.new_offset(0)
+      end
+      if (@high.is_a? DateTime) || (@high.is_a? Time)
+        @high = (@high.utc.to_time + seconds.seconds).to_datetime.new_offset(0)
+      end
+      self
+    end
+
     class << self
       # Get the object as it was stored in the database, and instantiate
       # this custom class from it.
@@ -25,6 +40,7 @@ module QDM
       def demongoize(object)
         return nil unless object
         object = object.symbolize_keys
+        fix_datetime(object)
         QDM::Interval.new(object[:low], object[:high], object[:lowClosed], object[:highClosed]) if object.is_a?(Hash)
       end
 
@@ -36,11 +52,18 @@ module QDM
         when QDM::Interval then object.mongoize
         when Hash
           object = object.symbolize_keys
+          fix_datetime(object)
           QDM::Interval.new(object[:low], object[:high], object[:lowClosed], object[:highClosed]).mongoize
         else object
         end
       end
 
+      def fix_datetime(object)
+        # Cast to DateTime if it is a string representing a DateTime
+        object[:low] = DateTime.parse(object[:low]) if (object[:low].is_a? String) && DateTime.parse(object[:low])
+        object[:high] = DateTime.parse(object[:high]) if (object[:high].is_a? String) && DateTime.parse(object[:high])
+      end
+
       # Converts the object that was supplied to a criteria and converts it
       # into a database friendly form.
       def evolve(object)

data/app/models/qdm/patient.rb

@@ -29,6 +29,17 @@ module QDM
       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.new_offset(0)
+      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')

data/app/models/qdm/tacoma/individual_result.rb

@@ -0,0 +1,39 @@
+module QDM
+  # IndividualResult stores the patient-level (population/clause) results for a patient/measure combination
+  class IndividualResult
+    include Mongoid::Document
+    include Mongoid::Timestamps
+
+    # This is the Mongoid equivalent of the Mongoose "enum" attribute for :state. Throws an error if you try to assign a value that's not in this array.
+    validates_inclusion_of :state, in: %w[queued running complete cancelled failed]
+
+    # Population Attributes
+    field :STRAT, type: Integer
+    field :IPP, type: Integer
+    field :DENOM, type: Integer
+    field :NUMER, type: Integer
+    field :NUMEX, type: Integer
+    field :DENEX, type: Integer
+    field :DENEXCEP, type: Integer
+    field :MSRPOPL, type: Integer
+    field :OBSERV, type: Float
+    field :MSRPOPLEX, type: Integer
+
+    # Result Attributes
+    field :clause_results, type: Hash
+    field :episode_results, type: Hash
+    field :statement_results, type: Hash
+
+    # This field is for application specific information only. If both Bonnie and
+    # Cypress use a common field, it should be made a field on this model,
+    # and not put into extendedData.
+    field :extendedData, type: Hash
+
+    # Calculation state attributes
+    field :state, type: String, default: 'queued'
+
+    # Relations to other model classes
+    belongs_to :measure
+    belongs_to :patient
+  end
+end

data/app/models/qdm/tacoma/measure.rb

@@ -74,7 +74,7 @@ module QDM
     # Relations to other model classes
     belongs_to :user
     belongs_to :bundle, class_name: 'HealthDataStandards::CQM::Bundle'
-    has_and_belongs_to_many :records, inverse_of: nil
+    has_and_belongs_to_many :patients, inverse_of: nil
     has_one :package, class_name: 'CqlMeasurePackage', inverse_of: :measure, dependent: :destroy
 
     scope :by_measure_id, ->(id) { where('measure_id' => id) }

data/cqm-models.gemspec

@@ -4,7 +4,7 @@ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 
 Gem::Specification.new do |spec|
   spec.name          = 'cqm-models'
-  spec.version       = '0.7.7'
+  spec.version       = '0.8.0'
   spec.authors       = ['aholmes@mitre.org', 'mokeefe@mitre.org', 'lades@mitre.org']
 
   spec.summary       = 'Mongo models that correspond to the QDM specification.'