qiprofile/app/javascripts/tnm.coffee

Quantitative Imaging Profile ( QiPr) web application

define ['angular', 'lodash', 'breast', 'sarcoma'], (ng, _) ->
  tnm = ng.module 'qiprofile.tnm', ['qiprofile.breast', 'qiprofile.sarcoma']

  tnm.factory 'TNM', ['Breast', 'Sarcoma', (Breast, Sarcoma) ->
    # The supported tumor type-specific services.
    TUMOR_TYPE_SERVICES =
      Breast: Breast
      Sarcoma: Sarcoma

    # @param tumorType the tumor type name, e.g. 'Breast'
    # @returns the tumorTypeService factory for that tumor type
    tumorTypeService = (tumorType) ->
      TUMOR_TYPE_SERVICES[tumorType] or
        throw new ReferenceError("Unsupported tumor type: #{ tumorType }")

    # Define here for reuse below.
    _summaryGrade = (tnm) ->
      # Calculates the cumulative grade as the sum of the component
      # tumor type factory SCORES property values.
      #
      # @param tnm the TNM object
      # @returns the cumulative grade, or null if a score is missing
      cumulativeGrade = ->
        accumulate = (sum, prop) ->
          sum + grade[prop]

        return null unless grade?
        props = tumorTypeService(tnm.tumorType).Grade.SCORES
        if _.every(props, (prop) -> grade[prop]?)
          _.reduce(props, accumulate, 0)
        else
          null

      grade = tnm.grade
      if not grade?
        return null
      # The sum of the relevant grade properties.
      cGrade = cumulativeGrade()
      if not cGrade? then return null
      # The tumor type grade ranges.
      ranges = tumorTypeService(tnm.tumorType).Grade.RANGES
      inRange = (range) -> cGrade in range
      index = _.findIndex(ranges, inRange)
      if index < 0
        throw new ReferenceError("Unsupported #{ tnm.tumorType }" +
                                 " cumulative grade: #{ cGrade }")

      # Return the one-based summary grade value.
      1 + index

    # @param size the size composite object
    # @returns the standard size string, e.g. 'p2b'
    # @throws Error if the tumorSize property value is missing
    formatSize: (size) ->
      sizeSuffix = ->
        inSituSuffix = (inSitu) ->
          if size.inSitu.invasiveType is 'ductal'
            'is(DCIS)'
          else if size.inSitu.invasiveType is 'lobular'
            'is(LCIS)'
          else
            'is'

        # The size suffix can be a, b, c or is.
        # in situ (is) can be modified with the invasive
        # type (ductal or lobular).
        if size.inSitu?
          inSituSuffix(size.inSitu)
        else if size.suffix?
          size.suffix
        else
          ''

      if not size.tumorSize?
        throw new Error("The TNM tumor size is missing")
      prefix = size.prefix or ''
      suffix  = sizeSuffix()
      "#{ prefix }#{ size.tumorSize }#{ suffix }"

    # Calculates the summary grade based on the cumulative grade
    # as defined in the tumor type factory RANGES lookup table.
    #
    # @param grade the grade composite object
    # @returns the summary grade
    # @throws ReferenceError if the grade scores are not supported
    summaryGrade: _summaryGrade

    # Calculates the tumor stage for the given TNM composite
    # object.
    #
    # This function returns the cancer stage as a string
    # consisting of a digit in the range 1 to 4 optionally
    # followed by a suffix A, B or C. This facilitates
    # accurate comparison, in contrast to the roman numeral
    # grade, e.g. '1A' < '2B' , but 'IA' > 'IIB'.
    # The romanize filter can be used to display the stage
    # in the standard archaic medical format.
    #
    # @param tnm the TNM object.
    # @returns the cancer stage object
    stage: (tnm) ->
      grade = _summaryGrade(tnm)
      # Delegate to the tumor type service.
      tumorTypeService(tnm.tumorType).stage(tnm, grade)
  ]