Class: HealthDataStandards::Import::CCR::SectionImporter

Inherits:
Object
  • Object
show all
Defined in:
lib/health-data-standards/import/ccr/section_importer.rb

Overview

Class that can be used to create an importer for a section of a ASTM CCR document. It usually operates by selecting all CCR entries in a section and then creates entries for them.

Direct Known Subclasses

ProductImporter, ResultImporter, SimpleImporter

Constant Summary collapse

CODE_SYSTEM_MAP = 
{
  "lnc"       => "LOINC",
  "loinc"     => "LOINC",
  "cpt"       => "CPT",
  "cpt-4"     => "CPT",
  "sct"       => "SNOMED-CT",
  "snomedct"  => "SNOMED-CT",
  "snomed-ct" => "SNOMED-CT",
  "rxnorm"    => "RxNorm",
  "i9cdx"     => "ICD-9-CM",
  "icd-9-cm"  => "ICD-9-CM",
  "icd9-cm"   => "ICD-9-CM",
   "icd9"      => "ICD-9-CM",
  "icd10-cm"   => "ICD-9-CM",
  "icd10"      => "ICD-9-CM",
  "cvx"        => "CVX",
  "hcpcs"      => "HCPCS",
  "cdc"        => "CDC-RE",
  "CDC"        => "CDC-RE",
  "cdc-re"     => "CDC-RE"

}

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(entry_xpath, section_name) ⇒ SectionImporter

Creates a new SectionImporter

Parameters:

  • entry_xpath (String) —

    An XPath expression that can be used to find the desired entries

  • section_name (String) —

    name of the section. There is some section-dependent processing



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 34

def initialize(entry_xpath,  section_name)
  @entry_xpath = entry_xpath
  @section_name = section_name
  @check_for_usable = true               # Pilot tools will set this to false
end

Instance Attribute Details

#check_for_usable ⇒ Object

Returns the value of attribute check_for_usable.



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 30

def check_for_usable
  @check_for_usable
end

Instance Method Details

#create_entries(doc) ⇒ Array

Traverses that ASTM CCR document passed in using XPath and creates an Array of Entry objects based on what it finds

Parameters:

  • doc (Nokogiri::XML::Document) —

    It is expected that the root node of this document will have the “ccr” namespace registered to “urn:astm-org:CCR” measure definition

Returns:

  • (Array) —

    will be a list of Entry objects



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 125

def create_entries(doc)
  return nil
end

#extract_codes(parent_element, entry) ⇒ Object

Add the codes from a <Code> block to an Entry



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 66

def extract_codes(parent_element, entry)
  codes = parent_element.xpath("./ccr:Description/ccr:Code")
  entry.description = ""
  if (parent_element.at_xpath("./ccr:Description/ccr:Text") )
    entry.description = parent_element.at_xpath("./ccr:Description/ccr:Text").content
  end
  if codes.size > 0 
    found_code = true
    codes.each do |code|
      normalize_coding_system(code)
      entry.add_code(code.at_xpath("./ccr:Value").content, code.at_xpath("./ccr:CodingSystem").content)
    end
  end
end

#extract_dates(parent_element, entry) ⇒ Object 



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 87

def extract_dates(parent_element, entry)
  datetime = parent_element.at_xpath('./ccr:DateTime')
  if !datetime
    return
  end
   if datetime.at_xpath('./ccr:ExactDateTime')
    entry.time = extract_time(datetime.at_xpath('./ccr:ExactDateTime').content)
  end
  if datetime.at_xpath('./ccr:ApproximateDateTime')
    entry.time = extract_time(datetime.at_xpath('./ccr:ApproximateDateTime').content)
  end
  if datetime.at_xpath('./ccr:DateTimeRange/ccr:BeginRange')
    entry.start_time = extract_time(datetime.at_xpath('./ccr:DateTimeRange/ccr:BeginRange').content)
  end
  if datetime.at_xpath('./ccr:DateTimeRange/ccr:EndRange')
    entry.end_time = extract_time(datetime.at_xpath('./ccr:DateTimeRange/ccr:EndRange').content)
  end
end

#extract_status(parent_element, entry) ⇒ Object 



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 52

def extract_status(parent_element, entry)
  status_element = parent_element.at_xpath('./ccr:Status')
  if status_element
    status_text = parent_element.at_xpath('./ccr:Status/ccr:Text')
    return unless status_text
    status = status_text.content.downcase
    if %w(active inactive resolved).include?(status)
      entry.status = status.to_sym
    end
  end                                          
end

#extract_time(datetime) ⇒ Object

Time is supposed to be in iso8601, but seems like we need to handle simple YYYY-MM-DD as well



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 82

def extract_time(datetime)
  return unless datetime
  Time.parse(datetime).to_i rescue nil
end

#extract_value(parent_element, entry) ⇒ Object 



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 106

def extract_value(parent_element, entry)
  result_element = parent_element.at_xpath('./ccr:TestResult')
  if result_element
    value_element = result_element.at_xpath('./ccr:Value')
    value = value_element ? value_element.content : nil
    unit_element = result_element.at_xpath('./ccr:Units/ccr:Unit')
    unit = unit_element ? unit_element.content : nil
    if value
      entry.set_value(value, unit)
    end
  end
end

#normalize_coding_system(code) ⇒ Object

normalize_coding_system attempts to simplify analysis of the XML doc by normalizing the names of the coding systems. Input is a single “Code” node in the tree, and the side effect is to edit the CodingSystem subnode.

Parameters:

  • code (String) —

    • Input is a single “Code” node



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# File 'lib/health-data-standards/import/ccr/section_importer.rb', line 44

def normalize_coding_system(code)
  coding_system = code.xpath('./ccr:CodingSystem')[0].content.downcase
  coding_system_value = CODE_SYSTEM_MAP[coding_system]
  if(coding_system_value)
    code.xpath('./ccr:CodingSystem')[0].content = coding_system_value
  end
end