cql_qdm_patientapi 1.0.0

data/app/assets/javascripts/datatypes/substance.js.coffee

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+###
+@namespace scoping into the CQL_QDM namespace (all classes and
+their methods will be accessable through the CQL_QDM namespace)
+###
+@CQL_QDM ||= {}
+
+
+###
+Data elements that meet criteria using this datatype should document that the
+substance indicated by the QDM category and its corresponding value set was
+actually given to the patient.
+###
+class CQL_QDM.SubstanceAdministered extends CQL_QDM.QDMDatatype
+  ###
+  @param {Object} entry - the HDS data criteria object to convert
+  ###
+  constructor: (@entry) ->
+    super @entry
+    @_authorDatetime = CQL_QDM.Helpers.convertDateTime(@entry.start_time)
+    @_dosage = @entry.dose
+    @_frequency = @entry.frequency
+    @_negationRationale = @entry.negationReason
+    @_relevantPeriodLow = CQL_QDM.Helpers.convertDateTime(@entry.start_time)
+    if @entry.end_time
+      @_relevantPeriodHigh = CQL_QDM.Helpers.convertDateTime(@entry.end_time)
+    else
+      # No end time; high is set to infinity
+      @_relevantPeriodHigh = CQL_QDM.Helpers.infinityDateTime()
+    @_route = @entry.route
+    @_supply = @entry.supply
+
+  ###
+  Author date time is only present when this data type has been negated.
+  @returns {Date}
+  ###
+  authorDatetime: ->
+    @_authorDatetime
+
+  ###
+  @returns {Quantity}
+  ###
+  dosage: ->
+    if @_dosage?
+      new cql.Quantity({unit: @_dosage['unit'], value: @_dosage['value']})
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  frequency: ->
+    # TODO: Frequency currently not in HDS model.  Can probably add by calculating based off of dose & regimen
+    throw new Error('Bonnie does not currently support SubstanceAdministered.frequency')
+    if @_frequency?
+      new cql.Code(@_frequency.code, @_frequency.code_system)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  negationRationale: ->
+    if @_negationRationale?
+      new cql.Code(@_negationRationale.code, @_negationRationale.code_system)
+    else
+      null
+
+  ###
+  @returns {Interval<Date>}
+  ###
+  relevantPeriod: ->
+    low = @_relevantPeriodLow
+    high = @_relevantPeriodHigh
+    if low?
+      new cql.Interval(low, high)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  route: ->
+    if @_route?
+      new cql.Code(@_route.code, @_route.code_system)
+    else
+      null
+
+  ###
+  @returns {Quantity}
+  ###
+  supply: ->
+    if @_supply?
+      new cql.Quantity({unit: @_supply['unit'], value: @_supply['value']})
+    else
+      null
+
+
+###
+Data elements that meet criteria using this datatype should document a request
+for the substance indicated by the QDM category and its corresponding value set.
+###
+class CQL_QDM.SubstanceOrder extends CQL_QDM.QDMDatatype
+  ###
+  @param {Object} entry - the HDS data criteria object to convert
+  ###
+  constructor: (@entry) ->
+    super @entry
+    @_authorDatetime = CQL_QDM.Helpers.convertDateTime(@entry.start_time)
+    @_dosage = @entry.dose
+    @_frequency = @entry.frequency
+    @_method = @entry.method
+    @_negationRationale = @entry.negationReason
+    @_reason = @entry.reason
+    @_refills = @entry.refills
+    @_route = @entry.route
+    @_supply = @entry.supply
+
+  ###
+  @returns {Date}
+  ###
+  authorDatetime: ->
+    @_authorDatetime
+
+  ###
+  @returns {Quantity}
+  ###
+  dosage: ->
+    if @_dosage?
+      new cql.Quantity({unit: @_dosage['unit'], value: @_dosage['value']})
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  frequency: ->
+    # TODO: Frequency currently not in HDS model.  Can probably add by calculating based off of dose & regimen
+    throw new Error('Bonnie does not currently support SubstanceOrder.frequency')
+    if @_frequency?
+      new cql.Code(@_frequency.code, @_frequency.code_system)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  method: ->
+    if @_method?
+      new cql.Code(@_method.code, @_method.code_system)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  negationRationale: ->
+    if @_negationRationale?
+      new cql.Code(@_negationRationale.code, @_negationRationale.code_system)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  reason: ->
+    if @_reason?
+      new cql.Code(@_reason.code, @_reason.code_system)
+    else
+      null
+
+  ###
+  @returns {Integer}
+  ###
+  refills: ->
+    # TODO: Refills should represent 'The number of refills allowed by the prescription.'
+    throw new Error('Bonnie does not currently support SubstanceOrder.refills')
+
+  ###
+  @returns {Code}
+  ###
+  route: ->
+    if @_route?
+      new cql.Code(@_route.code, @_route.code_system)
+    else
+      null
+
+  ###
+  @returns {Quantity}
+  ###
+  supply: ->
+    if @_supply?
+      new cql.Quantity({unit: @_supply['unit'], value: @_supply['value']})
+    else
+      null
+
+
+###
+Data elements that meet criteria using this datatype should document a
+recommendation for the substance indicated by the QDM category and its
+corresponding value set.
+###
+class CQL_QDM.SubstanceRecommended extends CQL_QDM.QDMDatatype
+  ###
+  @param {Object} entry - the HDS data criteria object to convert
+  ###
+  constructor: (@entry) ->
+    super @entry
+    @_authorDatetime = CQL_QDM.Helpers.convertDateTime(@entry.start_time)
+    @_dosage = @entry.dose
+    @_frequency = @entry.frequency
+    @_method = @entry.method
+    @_negationRationale = @entry.negationReason
+    @_reason = @entry.reason
+    @_refills = @entry.refills
+    @_route = @entry.route
+    @_supply = @entry.supply
+
+  ###
+  @returns {Date}
+  ###
+  authorDatetime: ->
+    @_authorDatetime
+
+  ###
+  @returns {Quantity}
+  ###
+  dosage: ->
+    if @_dosage?
+      new cql.Quantity({unit: @_dosage['unit'], value: @_dosage['value']})
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  frequency: ->
+    # TODO: Frequency currently not in HDS model.  Can probably add by calculating based off of dose & regimen
+    throw new Error('Bonnie does not currently support SubstanceRecommended.frequency')
+    if @_frequency?
+      new cql.Code(@_frequency.code, @_frequency.code_system)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  method: ->
+    if @_method?
+      new cql.Code(@_method.code, @_method.code_system)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  negationRationale: ->
+    if @_negationRationale?
+      new cql.Code(@_negationRationale.code, @_negationRationale.code_system)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  reason: ->
+    if @_reason?
+      new cql.Code(@_reason.code, @_reason.code_system)
+    else
+      null
+
+  ###
+  @returns {Integer}
+  ###
+  refills: ->
+    # TODO: Refills should represent 'The number of refills allowed by the prescription.'
+    throw new Error('Bonnie does not currently support SubstanceRecommended.refills')
+
+  ###
+  @returns {Code}
+  ###
+  route: ->
+    if @_route?
+      new cql.Code(@_route.code, @_route.code_system)
+    else
+      null
+
+  ###
+  @returns {Quantity}
+  ###
+  supply: ->
+    if @_supply?
+      new cql.Quantity({unit: @_supply['unit'], value: @_supply['value']})
+    else
+      null

data/app/assets/javascripts/datatypes/symptom.js.coffee

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+###
+@namespace scoping into the CQL_QDM namespace (all classes and
+their methods will be accessable through the CQL_QDM namespace)
+###
+@CQL_QDM ||= {}
+
+
+###
+Data elements that meet criteria using this datatype should document the
+symptom and its corresponding value set. The onset datetime corresponds to the
+implicit start datetime of the datatype and the abatement datetime corresponds
+to the implicit stop datetime of the datatype. If the abatement datetime is
+null, then the symptom is considered to still be active. When this datatype is
+used with timing relationships, the criterion is looking for whether the
+symptom was active for the time frame indicated by the timing relationships.
+###
+class CQL_QDM.Symptom extends CQL_QDM.QDMDatatype
+  ###
+  @param {Object} entry - the HDS data criteria object to convert
+  ###
+  constructor: (@entry) ->
+    super @entry
+    @_prevalencePeriodLow = CQL_QDM.Helpers.convertDateTime(@entry.start_time)
+    if @entry.end_time
+      @_prevalencePeriodHigh = CQL_QDM.Helpers.convertDateTime(@entry.end_time)
+    else
+      # No end time; high is set to infinity
+      @_prevalencePeriodHigh = CQL_QDM.Helpers.infinityDateTime()
+    @_severity = @entry.severity
+
+  ###
+  @returns {Interval<Date>}
+  ###
+  prevalencePeriod: ->
+    low = @_prevalencePeriodLow
+    high = @_prevalencePeriodHigh
+    if low?
+      new cql.Interval(low, high)
+    else
+      null
+
+  ###
+  @returns {Code}
+  ###
+  severity: ->
+    if @_severity?
+      new cql.Code(@_severity.code, @_severity.code_system)
+    else
+      null

data/app/assets/javascripts/types/component.js.coffee

@@ -0,0 +1,71 @@
+###
+@namespace scoping into the CQL_QDM namespace (all classes and
+their methods will be accessable through the CQL_QDM namespace)
+###
+@CQL_QDM ||= {}
+
+###
+Represents a CQL 'component' for use in the CQL execution engine.
+###
+class CQL_QDM.Component
+  constructor: (component) ->
+    @_result = CQL_QDM.Helpers.formatResult(component.result)
+    @_code = new cql.Code(component.code.code, component.code.code_system)
+
+  exec: (ctx) ->
+    @
+  
+  toString: () ->
+    "#{@_result.toString()} '#{@_code.toString()}'"
+
+  ###
+  @returns {Code}
+  ###
+  code: ->
+    if @_code?
+      @_code
+    else
+      null
+
+  ###
+  The model_info_file also lists Integer, Decimal, DateTime, Time, and Ratio.
+  Decimal and Integer are covered under Quantity with a nil unit.
+  Ratio is not yet supported with CQL although it appears in the QDM model.
+  Time and Datetime are covered by Date
+  @returns {Code|Quantity}
+  ###
+  result: ->
+    if @_result?
+      @_result
+    else
+      null
+
+###
+Represents a CQL 'component' for Laboratory Test Performed, which has a reference range.
+###
+class CQL_QDM.ResultComponent extends CQL_QDM.Component
+  constructor: (component) ->
+    super(component)
+    referenceRangeLow = component.referenceRangeLow if component.referenceRangeLow.scalar    # {"scalar": scalar, "unit": unit}}
+    referenceRangeHigh = component.referenceRangeHigh if component.referenceRangeHigh.scalar 
+    referenceRangeLow_value = referenceRangeLow.scalar if referenceRangeLow
+    referenceRangeHigh_value = referenceRangeHigh.scalar if referenceRangeHigh
+
+    # If only one of low/high is defined, make interval with undefined endpoint
+    @_referenceRange = new cql.Interval(referenceRangeLow_value, referenceRangeHigh_value) if referenceRangeLow_value || referenceRangeHigh_value
+    # TODO: might need to deal with units in the future
+
+  exec: (ctx) ->
+    @
+
+  toString: () ->
+    "'#{@_referenceRange.toString()}'"
+
+  ###
+  @returns {Interval<Quantity>}
+  ###
+  referenceRange: ->
+    if @_referenceRange?
+      @_referenceRange
+    else
+      null

data/app/assets/javascripts/types/facility.js.coffee

@@ -0,0 +1,41 @@
+###
+@namespace scoping into the CQL_QDM namespace (all classes and
+their methods will be accessable through the CQL_QDM namespace)
+###
+@CQL_QDM ||= {}
+
+###
+Represents a CQL 'facility' for use in the CQL execution engine.
+###
+class CQL_QDM.FacilityLocation
+  constructor: (facility) ->
+    @_code = new cql.Code(facility.code.code, facility.code.code_system, undefined, facility.display)
+
+    locationPeriodLow = CQL_QDM.Helpers.convertDateTime(facility.locationPeriodLow) if facility.locationPeriodLow
+    locationPeriodHigh = CQL_QDM.Helpers.convertDateTime(facility.locationPeriodHigh) if facility.locationPeriodHigh
+    # If only one of Low/High is defined, make an interval with an undefined start or end
+    @_locationPeriod = new cql.Interval(locationPeriodLow, locationPeriodHigh) if locationPeriodLow || locationPeriodHigh
+
+  exec: (ctx) ->
+    @
+  
+  toString: () ->
+    "#{@_locationPeriod} '#{@_code.toString()}'"
+
+  ###
+  @returns {Code}
+  ###
+  code: ->
+    if @_code?
+      @_code
+    else
+      null
+
+  ###
+  @returns {Interval<Date>}
+  ###
+  locationPeriod: ->
+    if @_locationPeriod?
+      @_locationPeriod
+    else
+      null

data/app/assets/javascripts/types/id.js.coffee

@@ -0,0 +1,23 @@
+###
+@namespace scoping into the CQL_QDM namespace (all classes and
+their methods will be accessable through the CQL_QDM namespace)
+###
+@CQL_QDM ||= {}
+
+###
+Represents the QDM.Id used in the execution engine.
+###
+class CQL_QDM.Id
+  constructor: (@value, @namingSystem) ->
+
+###
+@returns {String}
+###
+namingSystem: ->
+  @namingSystem
+
+###
+@returns {String}
+###
+value: ->
+  @namingSystem

data/app/assets/javascripts/utils/helpers.js.coffee

@@ -0,0 +1,101 @@
+###
+@namespace scoping into the CQL_QDM namespace (all classes and
+their methods will be accessable through the CQL_QDM namespace)
+###
+@CQL_QDM ||= {}
+
+
+###
+Various helper methods.
+###
+class CQL_QDM.Helpers
+
+  ###
+  Used to convert a Bonnie date + time into a compatible cql DateTime.
+
+  @param {String} input - the date time to convert
+  @returns cql.DateTime
+  ###
+  @convertDateTime: (input) ->
+    if input?
+      if moment.utc(input, 'MM/DD/YYYY hh:mm A', true).isValid() || moment.utc(input, 'MM/DD/YYYY h:mm A', true).isValid()
+        cql.DateTime.fromDate(moment.utc(input, 'MM/DD/YYYY hh:mm A').toDate(), 0)
+      else
+        cql.DateTime.fromDate(moment.utc(input, 'X').toDate(), 0)
+    else
+      null
+
+  ###
+  Returns an 'end of range' cql.DateTime.
+  See Section 3.4.1 "System-Defined Types" in the CQL specification.
+
+  @returns cql.DateTime
+  ###
+  @infinityDateTime: ->
+    cql.DateTime.parse('9999-12-31T23:59:59.999+0000')
+
+  ###
+  For DateTime values makes sure value meets the CQL standard.
+  For scalar values:
+    - First checks that the value component is numeric
+    - Second for the unit component attempts to clean up freetext
+      to match a standard version.
+
+  @param {Result} input - the result object to be parsed into a Quantity
+  @returns cql.Quantity
+  ###
+  @formatResult: (input) ->
+    if input?
+      if input?.units == 'UnixTime'
+        CQL_QDM.Helpers.convertDateTime(input.scalar)
+      else if input.codes?
+        code_system = Object.keys(input.codes)?[0]
+        code = input.codes[code_system]?[0]
+        new cql.Code(code, code_system)
+      else if input.code?
+        code_system = input.code.code_system
+        code = input.code.code
+        new cql.Code(code, code_system)
+      # Check that the scalar portion is a number and the units are a non-zero length string.
+      else if (input.scalar?.match(/^[-+]?[0-9]*\.?[0-9]+$/) != null)
+        if input.units.length > 0
+          new cql.Quantity({unit: input.units , value: parseFloat(input.scalar)})
+        else
+          parseFloat(input.scalar)
+    else
+      null
+
+  ###
+  @returns {Array}
+  ###
+  @relatedTo: (relatedToInput) ->
+    relatedToArray = []
+    if relatedToInput?
+      for relatedTo in relatedToInput
+        if relatedTo?
+          relatedToArray.push new CQL_QDM.Id(relatedTo.referenced_id)
+    relatedToArray
+
+  ###
+  @returns {Array}
+  ###
+  @components: (componentsInput) ->
+    components = []
+    if componentsInput?
+      for value in componentsInput.values
+        if value?
+          components.push new CQL_QDM.Component(value)
+    components
+
+  ###
+  @returns {Array}
+  ###
+  @diagnoses: (diagnosesInput, principalDiagnosisInput) ->
+    diagnoses = []
+    if diagnosesInput?
+      for diagnosis in diagnosesInput.values
+        if diagnosis?
+          diagnoses.push new cql.Code(diagnosis.code, diagnosis.code_system)
+    if principalDiagnosisInput?
+      diagnoses.push new cql.Code(principalDiagnosisInput.code, principalDiagnosisInput.code_system)
+    diagnoses

data/bin/rails

@@ -0,0 +1,12 @@
+#!/usr/bin/env ruby
+# This command will automatically be run when you run "rails" with Rails 4 gems installed from the root of your application.
+
+ENGINE_ROOT = File.expand_path('../..', __FILE__)
+ENGINE_PATH = File.expand_path('../../lib/cql_qdm_patientapi/engine', __FILE__)
+
+# Set up gems listed in the Gemfile.
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+require 'bundler/setup' if File.exist?(ENV['BUNDLE_GEMFILE'])
+
+require 'rails/all'
+require 'rails/engine/commands'