Patient Importer - Comm from Provider to Provider - Wrong ID about health-data-standards HOT 2 OPEN

module HealthDataStandards
  module Import
    module Cat1

      # This class is the central location for taking a QRDA Cat 1 XML document and converting it
      # into the processed form we store in MongoDB. The class does this by running each measure
      # independently on the XML document
      #
      # This class is a Singleton. It should be accessed by calling PatientImporter.instance
      class PatientImporter
        alias_method :original_initialize, :initialize

        def initialize
          original_initialize

          # MONKEY PATCH: USING 1.129 (negative) instead of 1.29 (positive) for P2P Communication
          begin
            index = @section_importers[:procedures].find_index { |p| p.hqmf_oid == '2.16.840.1.113883.3.560.1.129'}

            if index.present?
              ptpcomm = @section_importers[:procedures][index]
              ptpcomm.hqmf_oid = '2.16.840.1.113883.3.560.1.29'
              @section_importers[:procedures][index] = ptpcomm

              puts "monkey patched initialize: #{@section_importers[:procedures][index].to_yaml}"
            else
              puts "MONKEY PATCH FAILED!"
            end

          rescue
            puts "Error #{$!}"
          end
        end

      end
    end
  end
end

module HealthDataStandards
  module Import
    module Cat1

      class PatientImporter
        alias_method :original_initialize, :initialize

        def initialize
          original_initialize

          # MONKEY PATCH: USING 1.129 (negative) instead of 1.29 (positive) for Provider To Provider Communication
          # MONKEY PATCH: USING 1.103 (negative) instead of 1.3 (positive) for Diagnostic Study, Performed
          # MONKEY PATCH: USING 1.131 (negative) instead of 1.31 (positive) for Communication: From Provider to Patient
          # MONKEY PATCH: USING 1.110 (negative) instead of 1.10 (positive) for Device, Applied
          # MONKEY PATCH: Missing Substance, Administered
          begin
            index = @section_importers[:procedures].find_index { |p| p.hqmf_oid == '2.16.840.1.113883.3.560.1.129'}

            if index.present?
              importer = generate_importer(Cat1::ProcedureImporter, nil, '2.16.840.1.113883.3.560.1.29') #comm from provider to provider
              @section_importers[:procedures][index] = importer

              # puts "monkey patched initialize: #{@section_importers[:procedures][index].to_yaml}"
            else
              puts "MONKEY PATCH FAILED! - 129"
            end

            index = @section_importers[:procedures].find_index { |p| p.hqmf_oid == '2.16.840.1.113883.3.560.1.103'}

            if index.present?
              importer = generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.18']", '2.16.840.1.113883.3.560.1.3', 'performed') #diagnostic study performed
              @section_importers[:procedures][index] = importer

              # puts "monkey patched initialize: #{@section_importers[:procedures][index].to_yaml}"
            else
              puts "MONKEY PATCH FAILED! - 103"
            end

            index = @section_importers[:procedures].find_index { |p| p.hqmf_oid == '2.16.840.1.113883.3.560.1.131'}

            if index.present?
              importer = generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.3']", '2.16.840.1.113883.3.560.1.31') #comm from provider to patient
              @section_importers[:procedures][index] = importer

              # puts "monkey patched initialize: #{@section_importers[:procedures][index].to_yaml}"
            else
              puts "MONKEY PATCH FAILED! - 131"
            end

            index = @section_importers[:medical_equipment].find_index { |p| p.hqmf_oid == '2.16.840.1.113883.3.560.1.110'}

            if index.present?
              importer = generate_importer(CDA::MedicalEquipmentImporter, "./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.7']", '2.16.840.1.113883.3.560.1.10', 'applied')
              @section_importers[:medical_equipment][index] = importer

              # puts "monkey patched initialize: #{@section_importers[:procedures][index].to_yaml}"
            else
              puts "MONKEY PATCH FAILED! - 110"
            end


            index = @section_importers[:medications].find_index { |p| p.hqmf_oid == '2.16.840.1.113883.3.560.1.14'}

            if index.present?
              importer = generate_importer(CDA::MedicationImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.16' and cda:text[not(contains(text(), 'Substance'))] ]", '2.16.840.1.113883.3.560.1.14', 'administered') #medication administered
              @section_importers[:medications][index] = importer

              importer = generate_importer(CDA::MedicationImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.16' and cda:text[contains(text(), 'Substance')] ]", '2.16.840.1.113883.3.560.1.64', 'administered') # substance administered
              @section_importers[:medications] << importer

              # puts "monkey patched initialize: #{@section_importers[:procedures][index].to_yaml}"
            else
              puts "MONKEY PATCH FAILED! - 14"
            end

          rescue  => e
            puts "OOPS! #{e.inspect}"
            puts e.backtrace
          end
        end

        # def import_sections(record, doc)
        #
        #   context = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']")
        #   nrh = CDA::NarrativeReferenceHandler.new
        #   nrh.build_id_map(doc)
        #   @section_importers.each do |section, entry_packages|
        #     entry_packages.each do |entry_package|
        #       puts "#{section.to_json} - #{entry_package.to_json} - #{entry_package.package_entries(context, nrh).to_json}" if section.to_s == 'procedures' && entry_package.package_entries(context, nrh).length > 0
        #       record.send(section) << entry_package.package_entries(context, nrh)
        #     end
        #   end
        #end

      end
    end
  end
end

module HealthDataStandards
  module Import
    module CDA
      class SectionImporter

        private

        alias_method :original_extract_code, :extract_code

        # MONKEY PATCH: Only return code_hash if a code was found (fix for codeClass="UNK")
        # MONKEY PATCH: template generators expect code_system not codeSystem
        def extract_code(parent_element, code_xpath, code_system=nil)
          code_hash = original_extract_code parent_element, code_xpath, code_system

          code_hash = nil unless code_hash.present? && code_hash['code'].present?

          if code_hash.present?
            code_hash['code_system'] = code_hash['codeSystem'] if code_hash['codeSystem']
            code_hash['code_system_oid'] = code_hash['codeSystemOid'] if code_hash['codeSystemOid']
          end

          code_hash
        end

      end
    end
  end
end

module HealthDataStandards
  module Import
    module Cat1
      class EntryPackage

        attr_accessor :oid_hash, :status_hash

        alias_method :original_initialize, :initialize

        def initialize (type, oid, stat = nil)
          begin
            if oid.is_a?(Hash)
              self.oid_hash = oid
              oid = oid[:positive]
            else
              self.oid_hash = { positive: oid, negative: find_negative(oid) }
            end

            if stat.is_a?(Hash)
              self.status_hash = stat
              stat = stat[:positive]
            else
              self.status_hash = { positive: stat }
              self.status_hash[:negative] = "not " + stat if stat.present?
            end

            return original_initialize(type, oid, stat)
          rescue => e
            puts "OOPS! #{e.inspect}"
            puts e.backtrace
          end
        end

        def find_negative(oid)
          neg_oid = oid.dup # copy
          ri = neg_oid.rindex('.')
          rn = neg_oid[ri + 1, 10].to_i

          if rn < 1000
            rn = rn + 100
          else
            rn = '1' + rn.to_s
          end

          neg_oid = neg_oid[0, ri + 1] + rn.to_s

          ret = oid # default ret if can't find

          by_id = HealthDataStandards::Export::QRDA::EntryTemplateResolver.hqmf_qrda_oid_map.select { |e|
            e['hqmf_oid'] == oid
          }

          if by_id.length == 1
            # found just one positive... let's do it

            negs = HealthDataStandards::Export::QRDA::EntryTemplateResolver.hqmf_qrda_oid_map.select { |e|
              e['qrda_oid'] == by_id[0]['qrda_oid'] && (e['hqmf_oid'] == neg_oid || e['hqmf_name'] == by_id[0]['hqmf_name'] + " not done")
            }

            if negs.length == 1
              ret = negs[0]['hqmf_oid']
              puts "  FOUND NEG FOR #{oid}: #{negs[0].to_json}"
              puts " NEG SET, BUT ID MISMATCH FOR #{oid}: #{ret} != #{neg_oid}" if neg_oid != ret
            else
              puts "  NO NEG FOR #{oid}: neg_by_name.length: #{negs.length}"
            end
          else
            puts "  NO NEG SET FOR #{oid}: by_id.length: #{by_id.length}"
          end

          #puts " NEG SET: #{ret} for #{oid}" if oid != ret

          return ret
        end

        def select_oid(entry)
          return self.oid_hash[:positive] unless entry.negation_ind
          return self.oid_hash[:negative] if entry.negation_ind
        end

        def select_status(entry)
          return self.status_hash[:positive] unless entry.negation_ind
          return self.status_hash[:negative] if entry.negation_ind
        end

        def package_entries (doc, nrh)
          entries = self.importer_type.create_entries(doc, nrh)
          entries.each do |entry|

            begin
              entry.oid = self.select_oid(entry)
              entry.status = self.select_status(entry)
            rescue
              "DOH! #{$!}"
            end

          end
          entries
        end
      end
    end
  end
end