Class: HealthDataStandards::Import::BulkRecordImporter

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

Class Method Summary collapse

Class Method Details

.import(xml_data, provider_map = {}) ⇒ Object 



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# File 'lib/health-data-standards/import/bulk_record_importer.rb', line 93

def self.import(xml_data, provider_map = {})
  doc = xml_data.kind_of?(Nokogiri::XML::Document) ? xml_data : Nokogiri::XML(xml_data)

  providers = []
  root_element_name = doc.root.name

  if root_element_name == 'ClinicalDocument'
    doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
    doc.root.add_namespace_definition('sdtc', 'urn:hl7-org:sdtc')

    if doc.at_xpath("/cda:ClinicalDocument/cda:templateId[@root='2.16.840.1.113883.3.88.11.32.1']")
      patient_data = C32::PatientImporter.instance.parse_c32(doc)
    elsif doc.at_xpath("/cda:ClinicalDocument/cda:templateId[@root='2.16.840.1.113883.10.20.22.1.2']")
      patient_data = CCDA::PatientImporter.instance.parse_ccda(doc)
    elsif doc.at_xpath("/cda:ClinicalDocument/cda:templateId[@root='2.16.840.1.113883.10.20.24.1.2']")
      patient_data = Cat1::PatientImporter.instance.parse_cat1(doc)
    else
      STDERR.puts("Unable to determinate document template/type of CDA document")
      return {status: 'error', message: "Document templateId does not identify it as a C32 or CCDA", status_code: 400}
    end

    record = Record.update_or_create(patient_data)

    begin
      providers = CDA::ProviderImporter.instance.extract_providers(doc, record)
    rescue Exception => e
      STDERR.puts "error extracting providers"
    end
  else
    return {status: 'error', message: 'Unknown XML Format', status_code: 400}
  end

  record.provider_performances = providers
  providers.each do |prov|
    prov.provider.ancestors.each do |ancestor|
      record.provider_performances.push(ProviderPerformance.new(start_date: prov.start_date, end_date: prov.end_date, provider: ancestor))
    end
  end
  if record.save
    return record
  end
end

.import_archive(file, failed_dir = nil) ⇒ Object 



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# File 'lib/health-data-standards/import/bulk_record_importer.rb', line 14

def self.import_archive(file, failed_dir=nil)
  begin
  failed_dir ||=File.join(File.dirname(file))

  patient_id_list = nil

  Zip::ZipFile.open(file.path) do |zipfile|
    zipfile.entries.each do |entry|
      if entry.name
        if entry.name.split("/").last == "patient_manifest.txt"
          patient_id_list = zipfile.read(entry.name)
          next
        end
      end
      next if entry.directory?
      data = zipfile.read(entry.name)
      status = self.import_file(entry.name,data,failed_dir)
      raise StandardError, status[:message] if status.is_a?(Hash) && status[:status] === 'error'
    end
  end

  missing_patients = []

  #if there was a patient manifest, theres a patient id list we need to load
  if patient_id_list
    patient_id_list.split("\n").each do |id|
      patient = Record.where(:medical_record_number => id).first
      if patient == nil
        missing_patients << id
      end
    end
  end

  missing_patients

rescue
  FileUtils.mkdir_p(failed_dir)
  FileUtils.cp(file,File.join(failed_dir,File.basename(file)))
  File.open(File.join(failed_dir,"#{file}.error"), 'w') do |f|
    f.puts($!.message)
    f.puts($!.backtrace)
  end
  raise $!
end
end

.import_directory(source_dir, failed_dir = nil) ⇒ Object 



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# File 'lib/health-data-standards/import/bulk_record_importer.rb', line 6

def self.import_directory(source_dir, failed_dir=nil)
  failed_dir ||= File.join(source_dir, '../', 'failed_imports')
  files = Dir.glob(File.join(source_dir, '*.*'))
  files.each do |file|
    self.import_file(file,File.new(file).read,failed_dir)
  end
end

.import_file(name, data, failed_dir, provider_map = {}) ⇒ Object 



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# File 'lib/health-data-standards/import/bulk_record_importer.rb', line 60

def self.import_file(name,data,failed_dir,provider_map={})
  begin
    ext = File.extname(name)
    if ext == ".json"
      self.import_json(data)
    else
      self.import(data)
    end
  rescue
    FileUtils.mkdir_p(File.dirname(File.join(failed_dir,name)))
    File.open(File.join(failed_dir,name),"w") do |f|
      f.puts(data)
    end
    File.open(File.join(failed_dir,"#{name}.error"),"w") do |f|
      f.puts($!.message)
      f.puts($!.backtrace)
    end
    raise $!
  end
end

.import_json(data, provider_map = {}) ⇒ Object 



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# File 'lib/health-data-standards/import/bulk_record_importer.rb', line 81

def self.import_json(data,provider_map = {})
  json = JSON.parse(data,:max_nesting=>100)
  record = Record.update_or_create(Record.new(json))
  providers = record.provider_performances
  providers.each do |prov|
    prov.provider.ancestors.each do |ancestor|
      record.provider_performances.push(ProviderPerformance.new(start_date: prov.start_date, end_date: prov.end_date, provider: ancestor))
    end
  end
  record.save!
end