Top Level Namespace

Defined Under Namespace

Modules: Formulary

Constant Summary collapse

FHIR_SERVER =

Read the const variables from options or set default value.

"https://davinci-drug-formulary-ri.logicahealth.org"
CONFORMANCE_DEFINITIONS_URL = 
options.conformance_url || "https://build.fhir.org/ig/HL7/davinci-pdex-formulary/branches/master/definitions.json.zip"
FAILED_UPLOAD = 
[]
FHIR_SERVER_BASE = 
options.fhir_server || "https://davinci-drug-formulary-ri.logicahealth.org"
PAYERS = 
[]
FORMULARIES = 
[]
LOCATIONS = 
[]
NDOUTS = 
[]

Instance Method Summary collapse

Instance Method Details

#extract_location_id_from_reference(reference) ⇒ Object 



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# File 'scripts/plan_specific_ndjson.rb', line 61

def extract_location_id_from_reference(reference)
  reference = [] if reference.nil?
  reference.map { |area| area[:reference].split("/").last }
end

#generate_bulk_export ⇒ Object

Generates the grouped bulk data export



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# File 'scripts/plan_specific_ndjson.rb', line 154

def generate_bulk_export
  # Delete the bulk_export directory if it exists.
  FileUtils.rm_rf("bulk_export")

  get_all_insurance_plans
  get_all_location_resources
  p "==============================================================="
  p "Creating the Bulk export folder output ..."
  generate_payer_bulk_data
  generate_formulary_bulk_data
end

#generate_export_json(output_directory, request, output) ⇒ Object

Constructs and write the export.json file to the specified destination



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# File 'scripts/plan_specific_ndjson.rb', line 95

def generate_export_json(output_directory, request, output)
  export = {
    transactionTime: Time.now.strftime("%FT%T%:z"),
    request: request,
    requiresAccessToken: false,
    output: output,
  }
  file_path = File.join(output_directory, "export.json")
  File.open(file_path, "w") do |file|
    file.write(JSON.pretty_generate(export))
  end
end

#generate_formulary_bulk_data ⇒ Object

Group each formulary resource with its associated Location, Basic, and MedicationKnowledge resources.



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# File 'scripts/plan_specific_ndjson.rb', line 137

def generate_formulary_bulk_data
  p "There are no Formulary resources available to generate bulk data." if FORMULARIES.empty?
  FORMULARIES.each do |formulary|
    NDOUTS.clear
    request = "#{FHIR_SERVER}/fhir/InsurancePlan/#{formulary[:id]}/$export"
    output_directory = File.join("bulk_export", formulary[:id])
    FileUtils.mkdir_p(output_directory)
    generate_ndjson("InsurancePlan", [formulary], output_directory)
    get_related_basic_and_medicationknowledge(formulary[:id], output_directory)

    location_ids = extract_location_id_from_reference(formulary[:coverageArea])
    get_related_locations(location_ids, output_directory)
    generate_export_json(output_directory, request, NDOUTS)
  end
end

#generate_ndjson(resource_type, resource_list, output_directory) ⇒ Object

Writing ndjson files for a given resource type



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# File 'scripts/plan_specific_ndjson.rb', line 73

def generate_ndjson(resource_type, resource_list, output_directory)
  p "==============================================================="
  p "Generating ndjson file of type #{resource_type}..."
  outfile = File.join(output_directory, "#{resource_type}.ndjson")
  ndout = {
    type: resource_type,
    url: "#{FHIR_SERVER}/resources/#{output_directory.split("/").last}/#{resource_type}.ndjson",
  }
  NDOUTS << ndout

  begin
    o = File.open(outfile, "w")
    p "Writing #{resource_list.size} #{resource_type} resource instances to #{outfile}..."
    resource_list.each { |instance| o.puts(JSON.generate(instance)) }
  rescue StandardError => e
    puts "An error occured when generating file #{outfile}: #{e.message}"
  ensure
    o.close
  end
end

#generate_payer_bulk_data ⇒ Object

Group payer insurance resources with their associated Formulary, Basic, MK, and Location resources



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# File 'scripts/plan_specific_ndjson.rb', line 109

def generate_payer_bulk_data
  p "There are no payer resources available to generate bulk data." if PAYERS.empty?

  PAYERS.each do |payer|
    NDOUTS.clear
    request = "#{FHIR_SERVER}/fhir/InsurancePlan/#{payer[:id]}/$export"
    output_directory = File.join("bulk_export", payer[:id])
    FileUtils.mkdir_p(output_directory)
    related_formularies_id = []
    payer[:coverage].each do |coverage|
      formulary = coverage[:extension].find { |ext| ext[:url] == "http://hl7.org/fhir/us/davinci-drug-formulary/StructureDefinition/usdf-FormularyReference-extension" }
      unless formulary.nil?
        related_formularies_id << formulary[:valueReference][:reference].split("/").last
      end
    end

    related_formularies = FORMULARIES.find_all { |formulary| related_formularies_id.include?(formulary[:id]) }
    related_formularies.prepend(payer)
    generate_ndjson("InsurancePlan", related_formularies, output_directory)

    related_formularies_id.each { |id| get_related_basic_and_medicationknowledge(id, output_directory) }
    location_ids = extract_location_id_from_reference(payer[:coverageArea])
    get_related_locations(location_ids, output_directory)
    generate_export_json(output_directory, request, NDOUTS)
  end
end

#get_all_insurance_plans ⇒ Object 



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# File 'scripts/plan_specific_ndjson.rb', line 23

def get_all_insurance_plans
  p "==============================================================="
  p "Reading all InsurancePlan resources..."
  plan_files = get_resource_json_files("output/InsurancePlan")
  plan_files.each do |json_file|
    resource = JSON.parse(File.read(json_file), symbolize_names: true)
    json_file.include?("Payer") ? PAYERS << resource : FORMULARIES << resource
  end
  p "Found a total of #{PAYERS.size} PAYERS and #{FORMULARIES.size} Formulary plans."
end

#get_all_location_resources ⇒ Object 



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# File 'scripts/plan_specific_ndjson.rb', line 34

def get_all_location_resources
  location_files = get_resource_json_files("location_resources")
  location_files.each do |json_file|
    LOCATIONS << JSON.parse(File.read(json_file), symbolize_names: true)
  end
end

#get_related_basic_and_medicationknowledge(formulary_id, output_directory) ⇒ Object

Get all Basic and MK resources linked to the given InsurancePlan

Parameters:

  • formulary_id (String) —

    , the plan id

  • output_directory (String) —

    , the directory where the ndjson file should be written



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# File 'scripts/plan_specific_ndjson.rb', line 44

def get_related_basic_and_medicationknowledge(formulary_id, output_directory)
  p "==============================================================="
  p "Getting all Basic and MedicationKnowledge related to Formulary with ID= #{formulary_id}..."
  id_digits = formulary_id.split("-").last
  basic_files = get_resource_json_files("output/Basic").select { |f_name| f_name.include?(id_digits) }
  basic_resources = basic_files.map { |json_f| JSON.parse(File.read(json_f), symbolize_names: true) }
  # Get the reference ids to retrieve related medication_knowledge_resources
  ref_ids = basic_resources.map { |resource| resource[:id].split("-").last }
  medication_knowledge_files = get_resource_json_files("output/MedicationKnowledge").select { |f_name| ref_ids.any? { |id| f_name.include?(id) } }
  medication_knowledge_resources = medication_knowledge_files.map { |json_f| JSON.parse(File.read(json_f), symbolize_names: true) }

  p "There are #{basic_resources.size} Basic resources and #{medication_knowledge_resources.size} MedicationKnowledge resources related to Formulary with ID = #{formulary_id}"

  generate_ndjson("Basic", basic_resources, output_directory)
  generate_ndjson("MedicationKnowledge", medication_knowledge_resources, output_directory)
end

#get_related_locations(location_ids, output_directory) ⇒ Object

Retrieve location resources with given ids



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# File 'scripts/plan_specific_ndjson.rb', line 67

def get_related_locations(location_ids, output_directory)
  specific_locations = LOCATIONS.find_all { |loc| location_ids.include?(loc[:id]) }
  generate_ndjson("Location", specific_locations, output_directory)
end

#get_resource_json_files(resource_directory) ⇒ Array [String]

Returns a list of resource file's names from the resource directory.

Parameters:

  • resource_directory (String) —

    , the directory name to search

Returns:

  • (Array [String]) —

    a list of resource file's names from the resource directory



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# File 'scripts/plan_specific_ndjson.rb', line 18

def get_resource_json_files(resource_directory)
  file_path = File.join(resource_directory, "*.json")
  file_names = Dir.glob(file_path)
end

#retry_failed_upload ⇒ Object 



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# File 'scripts/upload.rb', line 87

def retry_failed_upload
  n = FAILED_UPLOAD.size
  while !FAILED_UPLOAD.empty? && n > 0
    puts "#{FAILED_UPLOAD.count} resource(s) failed to upload. Retrying..."
    failed_upload_copy = FAILED_UPLOAD.dup
    FAILED_UPLOAD.clear
    failed_upload_copy.each do |resource|
      response = upload_resource(resource)
      FAILED_UPLOAD << resource unless response&.success?
    end
    n -= 1
  end
  puts "Ending the program ..."
  if FAILED_UPLOAD.empty?
    puts "All resources were uploaded successfully."
  else
    puts "#{FAILED_UPLOAD.count} resource(s) failed to upload"
  end
end

#upload_all_resources ⇒ Object

Runs all the upload methods



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# File 'scripts/upload.rb', line 108

def upload_all_resources
  upload_conformance_resources
  upload_sample_resources
  retry_failed_upload
end

#upload_conformance_resources ⇒ Object 



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# File 'scripts/upload.rb', line 21

def upload_conformance_resources
  definitions_file = Tempfile.new
  begin
    definitions_data = HTTParty.get(CONFORMANCE_DEFINITIONS_URL, verify: false)
    definitions_file.write(definitions_data)
  rescue => e
    puts "Unable to upload conformance definitions."
    puts "Error#upload_conformance_resources: #{e.message}"
    return
  ensure
    definitions_file.close
  end

  begin
    Zip::File.open(definitions_file.path) do |zip_file|
      conf_resources = zip_file.entries
        .select { |entry| entry.name.end_with? ".json" }
        .reject { |entry| entry.name.start_with? "ImplementationGuide" }
      puts "Uploading #{conf_resources.count} conformance resources..."
      conf_resources.each do |entry|
        resource = JSON.parse(entry.get_input_stream.read, symbolize_names: true)
        response = upload_resource(resource)
        FAILED_UPLOAD << resource unless response&.success?
      end
    end
  rescue => e
    puts "Error#upload_conformance_resources: #{e.message}"
    puts "Please provide a valid conformance URL"
  ensure
    definitions_file.unlink
  end
end

#upload_resource(resource) ⇒ Object 



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# File 'scripts/upload.rb', line 71

def upload_resource(resource)
  resource_type = resource[:resourceType]
  id = resource[:id]
  begin
    HTTParty.put(
      "#{FHIR_SERVER}/#{resource_type}/#{id}",
      body: resource.to_json,
      headers: { 'Content-Type': "application/json" },
    )
  rescue => e
    puts "An exception occured when trying to load the resource #{resource[:resource_type]}/#{resource[:id]}."
    puts "Error#upload_resource: #{e.message}"
    return
  end
end

#upload_sample_resources ⇒ Object 



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# File 'scripts/upload.rb', line 54

def upload_sample_resources
  location_file_path = File.join("location_resources", "*.json")
  file_path = File.join("output", "**/*.json")
  filenames = Dir.glob([file_path, location_file_path])
  # .partition { |filename| filename.include? "InsurancePlan" }
  # .flatten
  puts "Uploading #{filenames.length} resources"
  filenames.each_with_index do |filename, index|
    resource = JSON.parse(File.read(filename), symbolize_names: true)
    response = upload_resource(resource)
    FAILED_UPLOAD << resource unless response&.success?
    if index % 100 == 0
      puts "#{FAILED_UPLOAD.count} out of #{index + 1} attempted resources failed to be uploaded successfully."
    end
  end
end