us_core_test_kit 0.1.0

data/lib/us_core_test_kit/search_test.rb

@@ -0,0 +1,686 @@
+require_relative 'date_search_validation'
+require_relative 'fhir_resource_navigation'
+require_relative 'search_test_properties'
+
+module USCoreTestKit
+  module SearchTest
+    extend Forwardable
+    include DateSearchValidation
+    include FHIRResourceNavigation
+
+    def_delegators 'self.class', :metadata, :provenance_metadata, :properties
+    def_delegators 'properties',
+                   :resource_type,
+                   :search_param_names,
+                   :saves_delayed_references?,
+                   :first_search?,
+                   :fixed_value_search?,
+                   :possible_status_search?,
+                   :test_medication_inclusion?,
+                   :test_post_search?,
+                   :token_search_params,
+                   :test_reference_variants?,
+                   :params_with_comparators,
+                   :multiple_or_search_params
+
+    def all_search_params
+      @all_search_params ||=
+        patient_id_list.each_with_object({}) do |patient_id, params|
+          params[patient_id] ||= []
+          new_params =
+            if fixed_value_search?
+              fixed_value_search_param_values.map { |value| fixed_value_search_params(value, patient_id) }
+            else
+              [search_params_with_values(patient_id)]
+            end
+          new_params.reject! do |params|
+            params.any? { |_key, value| value.blank? }
+          end
+
+          params[patient_id].concat(new_params)
+        end
+    end
+
+    def all_provenance_revinclude_search_params
+      @all_provenance_revinclude_search_params ||=
+        all_search_params.transform_values! do |params_list|
+          params_list.map { |params| params.merge(_revinclude: 'Provenance:target') }
+        end
+    end
+
+    def any_valid_search_params?(search_params)
+      search_params.any? { |_patient_id, params| params.present? }
+    end
+
+    def run_provenance_revinclude_search_test
+      # TODO: skip if not supported?
+      skip_if !any_valid_search_params?(all_provenance_revinclude_search_params), unable_to_resolve_params_message
+
+      provenance_resources =
+        all_provenance_revinclude_search_params.flat_map do |_patient_id, params_list|
+          params_list.flat_map do |params|
+            fhir_search resource_type, params: params
+
+            perform_search_with_status(params, patient_id) if response[:status] == 400 && possible_status_search?
+
+            check_search_response
+
+            fetch_all_bundled_resources(additional_resource_types: ['Provenance'])
+              .select { |resource| resource.resourceType == 'Provenance' }
+          end
+        end
+
+      scratch_provenance_resources[:all] ||= []
+      scratch_provenance_resources[:all].concat(provenance_resources)
+
+      save_delayed_references(provenance_resources, 'Provenance')
+
+      skip_if provenance_resources.empty?, no_resources_skip_message('Provenance')
+    end
+
+    def run_search_test
+      # TODO: skip if not supported?
+      skip_if !any_valid_search_params?(all_search_params), unable_to_resolve_params_message
+
+      resources_returned =
+        all_search_params.flat_map do |patient_id, params_list|
+          params_list.flat_map { |params| perform_search(params, patient_id) }
+        end
+
+      skip_if resources_returned.empty?, no_resources_skip_message
+
+      perform_multiple_or_search_test if multiple_or_search_params.present?
+    end
+
+    def perform_search(params, patient_id)
+      fhir_search resource_type, params: params
+
+      perform_search_with_status(params, patient_id) if response[:status] == 400 && possible_status_search?
+
+      check_search_response
+
+      resources_returned =
+        fetch_all_bundled_resources.select { |resource| resource.resourceType == resource_type }
+
+      return [] if resources_returned.blank?
+
+      perform_comparator_searches(params, patient_id) if params_with_comparators.present?
+
+      filter_devices(resources_returned) if resource_type == 'Device'
+
+      if first_search?
+        all_scratch_resources.concat(resources_returned).uniq!
+        scratch_resources_for_patient(patient_id).concat(resources_returned).uniq!
+      end
+
+      resources_returned.each do |resource|
+        check_resource_against_params(resource, params)
+      end
+
+      save_delayed_references(resources_returned) if saves_delayed_references?
+
+      return resources_returned if all_search_variants_tested?
+
+      perform_post_search(resources_returned, params) if test_post_search?
+      test_medication_inclusion(resources_returned, params, patient_id) if test_medication_inclusion?
+      perform_reference_with_type_search(params, resources_returned.count) if test_reference_variants?
+      perform_search_with_system(params, patient_id) if token_search_params.present?
+
+      resources_returned
+    end
+
+    def perform_post_search(get_search_resources, params)
+      fhir_search resource_type, params: params, search_method: :post
+
+      check_search_response
+
+      post_search_resources = fetch_all_bundled_resources.select { |resource| resource.resourceType == resource_type }
+      get_resource_count = get_search_resources.length
+      post_resource_count = post_search_resources.length
+
+      search_variant_test_records[:post_variant] = true
+
+      assert get_resource_count == post_resource_count,
+             "Expected search by POST to return the same results as search by GET, " \
+             "but GET search returned #{get_resource_count} resources, and POST search " \
+             "returned #{post_resource_count} resources."
+    end
+
+    def filter_devices(resources)
+      codes_to_include = implantable_device_codes&.split(',')&.map(&:strip)
+      return resources if codes_to_include.blank?
+
+      resources.select! do |resource|
+        resource&.type&.coding&.any? { |coding| codes_to_include.include?(coding.code) }
+      end
+    end
+
+    def search_and_check_response(params, resource_type = self.resource_type)
+      fhir_search resource_type, params: params
+
+      check_search_response
+    end
+
+    def check_search_response
+      assert_response_status(200)
+      assert_resource_type(:bundle)
+      # NOTE: how do we want to handle validating Bundles?
+    end
+
+    def search_variant_test_records
+      @search_variant_test_records ||= initial_search_variant_test_records
+    end
+
+    def initial_search_variant_test_records
+      {}.tap do |records|
+        records[:post_variant] = false if test_post_search?
+        records[:medication_inclusion] = false if test_medication_inclusion?
+        records[:reference_variants] = false if test_reference_variants?
+        records[:token_variants] = false if token_search_params.present?
+        records[:comparator_searches] = Set.new if params_with_comparators.present?
+      end
+    end
+
+    def all_search_variants_tested?
+      search_variant_test_records.all? { |_variant, tested| tested.present? } &&
+        all_comparator_searches_tested?
+    end
+
+    def all_comparator_searches_tested?
+      return true if params_with_comparators.blank?
+
+      Set.new(params_with_comparators) == search_variant_test_records[:comparator_searches]
+    end
+
+    def date_comparator_value(comparator, date)
+      date = date.start || date.end if date.is_a? FHIR::Period
+      case comparator
+      when 'lt', 'le'
+        comparator + (DateTime.xmlschema(date) + 1).xmlschema
+      when 'gt', 'ge'
+        comparator + (DateTime.xmlschema(date) - 1).xmlschema
+      else
+        # ''
+        raise "Unsupported comparator '#{comparator}'"
+      end
+    end
+
+    def required_comparators(name)
+      metadata
+        .search_definitions
+        .dig(name.to_sym, :comparators)
+        .select { |_comparator, expectation| expectation == 'SHALL' }
+        .keys
+        .map(&:to_s)
+    end
+
+    def perform_comparator_searches(params, patient_id)
+      params_with_comparators.each do |name|
+        next if search_variant_test_records[:comparator_searches].include? name
+
+        required_comparators(name).each do |comparator|
+          path = search_param_path(name)
+          date_element = find_a_value_at(scratch_resources_for_patient(patient_id), path)
+          params_with_comparator = params.merge(name => date_comparator_value(comparator, date_element))
+
+          search_and_check_response(params_with_comparator)
+
+          fetch_all_bundled_resources
+            .each { |resource| check_resource_against_params(resource, params_with_comparator) }
+        end
+
+        search_variant_test_records[:comparator_searches] << name
+      end
+    end
+
+    def perform_reference_with_type_search(params, resource_count)
+      return if resource_count == 0
+      return if search_variant_test_records[:reference_variants]
+
+      new_search_params = params.merge('patient' => "Patient/#{params['patient']}")
+      search_and_check_response(new_search_params)
+
+      new_resource_count =
+        fetch_all_bundled_resources
+          .select { |resource| resource.resourceType == resource_type }
+          .count
+
+      assert new_resource_count == resource_count,
+             "Expected search by `#{params['patient']}` to to return the same results as searching " \
+             "by `#{new_search_params['patient']}`, but found #{resource_count} resources with " \
+             "`#{params['patient']}` and #{new_resource_count} with `#{new_search_params['patient']}`"
+
+      search_variant_test_records[:reference_variants] = true
+    end
+
+    def perform_search_with_system(params, patient_id)
+      return if search_variant_test_records[:token_variants]
+
+      new_search_params = token_search_params.each_with_object({}) do |name, search_params|
+        search_params[name] = search_param_value(name, patient_id, include_system: true)
+      end
+      return if new_search_params.any? { |_name, value| value.blank? }
+
+      search_params = params.merge(new_search_params)
+      search_and_check_response(search_params)
+
+      resources_returned =
+        fetch_all_bundled_resources
+          .select { |resource| resource.resourceType == resource_type }
+
+      assert resources_returned.present?, "No resources were returned when searching by `system|code`"
+
+      search_variant_test_records[:token_variants] = true
+    end
+
+    def perform_search_with_status(
+          original_params,
+          patient_id,
+          status_search_values: self.status_search_values,
+          resource_type: self.resource_type
+        )
+      assert resource.is_a?(FHIR::OperationOutcome), "Server returned a status of 400 without an OperationOutcome"
+      # TODO: warn about documenting status requirements
+      status_search_values.flat_map do |status_value|
+        search_params = original_params.merge("#{status_search_param_name}": status_value)
+
+        search_and_check_response(search_params)
+
+        entries = resource.entry.select { |entry| entry.resource.resourceType == resource_type }
+
+        if entries.present?
+          original_params.merge!("#{status_search_param_name}": status_value)
+          break
+        end
+      end
+    end
+
+    def status_search_param_name
+      @status_search_param_name ||=
+        metadata.search_definitions.keys.find { |key| key.to_s.include? 'status' }
+    end
+
+    def status_search_values
+      default_search_values(status_search_param_name)
+    end
+
+    def default_search_values(param_name)
+      definition = metadata.search_definitions[param_name]
+      return [] if definition.blank?
+
+      definition[:multiple_or] == 'SHALL' ? [definition[:values].join(',')] : [definition[:values]]
+    end
+
+
+    def perform_multiple_or_search_test
+      resolved_one = false
+
+      all_search_params.each do |patient_id, params_list|
+        next unless params_list.present?
+        
+        search_params = params_list.first
+        existing_values = {}
+        missing_values = {}
+
+        multiple_or_search_params.each do |param_name|
+          search_value = default_search_values(param_name.to_sym)
+          search_params = search_params.merge("#{param_name}" => search_value)
+          existing_values[param_name.to_sym] = scratch_resources_for_patient(patient_id).map(&param_name.to_sym).compact.uniq
+        end
+
+        # skip patient without multiple-or values
+        next if existing_values.values.any?(&:empty?)
+
+        resolved_one = true
+
+        search_and_check_response(search_params)
+
+        resources_returned =
+          fetch_all_bundled_resources
+            .select { |resource| resource.resourceType == resource_type }
+
+        multiple_or_search_params.each do |param_name|
+          missing_values[param_name.to_sym] = existing_values[param_name.to_sym] - resources_returned.map(&param_name.to_sym)
+        end
+
+        missing_value_message = missing_values
+          .reject { |_param_name, missing_value| missing_value.empty? }
+          .map { |param_name, missing_value| "#{missing_value.join(',')} values from #{param_name}" }
+          .join(' and ')
+
+        assert missing_value_message.blank?, "Could not find #{missing_value_message} in any of the resources returned for Patient/#{patient_id}"
+
+        break if resolved_one
+      end
+    end
+
+    def test_medication_inclusion(medication_requests, params, patient_id)
+      return if search_variant_test_records[:medication_inclusion]
+
+      scratch[:medication_resources] ||= {}
+      scratch[:medication_resources][:all] ||= []
+      scratch[:medication_resources][patient_id] ||= []
+      scratch[:medication_resources][:contained] ||= []
+
+      requests_with_external_references =
+        medication_requests
+          .select { |request| request&.medicationReference&.present? }
+          .reject { |request| request&.medicationReference&.reference&.start_with? '#' }
+
+      contained_medications =
+        medication_requests
+          .select { |request| request&.medicationReference&.reference&.start_with? '#' }
+          .flat_map(&:contained)
+          .select { |resource| resource.resourceType == 'Medication' }
+
+      scratch[:medication_resources][:all] += contained_medications
+      scratch[:medication_resources][patient_id] += contained_medications
+      scratch[:medication_resources][:contained] += contained_medications
+
+      return if requests_with_external_references.blank?
+
+      search_params = params.merge(_include: 'MedicationRequest:medication')
+
+      search_and_check_response(search_params)
+
+      medications = fetch_all_bundled_resources.select { |resource| resource.resourceType == 'Medication' }
+      assert medications.present?, 'No Medications were included in the search results'
+
+      medications.uniq!(&:id)
+
+      scratch[:medication_resources][:all] += medications
+      scratch[:medication_resources][patient_id] += medications
+
+      search_variant_test_records[:medication_inclusion] = true
+    end
+
+    def all_scratch_resources
+      scratch_resources[:all] ||= []
+    end
+
+    def scratch_resources_for_patient(patient_id)
+      return all_scratch_resources if patient_id.nil?
+
+      scratch_resources[patient_id] ||= []
+    end
+
+    def references_to_save(resource_type = nil)
+      reference_metadata = resource_type == 'Provenance' ? provenance_metadata : metadata
+      reference_metadata.delayed_references
+    end
+
+    def fixed_value_search_param_name
+      (search_param_names - ['patient']).first
+    end
+
+    def fixed_value_search_param_values
+      metadata.search_definitions[fixed_value_search_param_name.to_sym][:values]
+    end
+
+    def fixed_value_search_params(value, patient_id)
+      search_param_names.each_with_object({}) do |name, params|
+        patient_id_param?(name) ? params[name] = patient_id : params[name] = value
+      end
+    end
+
+    def search_params_with_values(patient_id)
+      search_param_names.each_with_object({}) do |name, params|
+        value = patient_id_param?(name) ? patient_id : search_param_value(name, patient_id)
+        params[name] = value
+      end
+    end
+
+    def patient_id_list
+      return [nil] unless respond_to? :patient_ids
+
+      patient_ids.split(',').map(&:strip)
+    end
+
+    def patient_search?
+      search_param_names.any? { |name| patient_id_param? name }
+    end
+
+    def patient_id_param?(name)
+      name == 'patient' || (name == '_id' && resource_type == 'Patient')
+    end
+
+    def search_param_path(name)
+      path = metadata.search_definitions[name.to_sym][:path]
+      path == 'class' ? 'local_class' : path
+    end
+
+    def all_search_params_present?(params)
+      params.all? { |_name, value| value.present? }
+    end
+
+    def array_of_codes(array)
+      array.map { |name| "`#{name}`" }.join(', ')
+    end
+
+    def unable_to_resolve_params_message
+      "Could not find values for all search params #{array_of_codes(search_param_names)}"
+    end
+
+    def empty_search_params_message(empty_search_params)
+      "Could not find values for the search parameters #{array_of_codes(empty_search_params.keys)}"
+    end
+
+    def no_resources_skip_message(resource_type = self.resource_type)
+      "No #{resource_type} resources appear to be available. " \
+      "Please use patients with more information"
+    end
+
+    def fetch_all_bundled_resources(
+          reply_handler: nil,
+          max_pages: 20,
+          additional_resource_types: [],
+          resource_type: self.resource_type
+        )
+      page_count = 1
+      resources = []
+      bundle = resource
+
+      until bundle.nil? || page_count == max_pages
+        resources += bundle&.entry&.map { |entry| entry&.resource }
+        next_bundle_link = bundle&.link&.find { |link| link.relation == 'next' }&.url
+        reply_handler&.call(response)
+
+        break if next_bundle_link.blank?
+
+        reply = fhir_client.raw_read_url(next_bundle_link)
+
+        store_request('outgoing') { reply }
+        error_message = cant_resolve_next_bundle_message(next_bundle_link)
+
+        assert_response_status(200)
+        assert_valid_json(reply.body, error_message)
+
+        bundle = fhir_client.parse_reply(FHIR::Bundle, fhir_client.default_format, reply)
+
+        page_count += 1
+      end
+
+      valid_resource_types = [resource_type, 'OperationOutcome'].concat(additional_resource_types)
+      valid_resource_types << 'Medication' if resource_type == 'MedicationRequest'
+
+      all_valid_resource_types =
+        resources.all? { |entry| valid_resource_types.include? entry.resourceType }
+
+      assert all_valid_resource_types,
+             "All resources returned must be of the type: #{valid_resource_types.join(', ')}"
+
+      resources
+    end
+
+    def cant_resolve_next_bundle_message(link)
+      "Could not resolve next bundle: #{link}"
+    end
+
+    def search_param_value(name, patient_id, include_system: false)
+      path = search_param_path(name)
+      element = find_a_value_at(scratch_resources_for_patient(patient_id), path)
+      search_value =
+        case element
+        when FHIR::Period
+          if element.start.present?
+            'gt' + (DateTime.xmlschema(element.start) - 1).xmlschema
+          else
+            end_datetime = get_fhir_datetime_range(element.end)[:end]
+            'lt' + (end_datetime + 1).xmlschema
+          end
+        when FHIR::Reference
+          element.reference
+        when FHIR::CodeableConcept
+          if include_system
+            coding =
+              find_a_value_at(element, 'coding') { |coding| coding.code.present? && coding.system.present? }
+            coding.present? ? "#{coding.system}|#{coding.code}" : nil
+          else
+            find_a_value_at(element, 'coding.code')
+          end
+        when FHIR::Identifier
+          if include_system
+            identifier = find_a_value_at(scratch_resources_for_patient(patient_id), path) do |identifier|
+              identifier.value.present? && identifier.system.present?
+            end
+            identifier.present? ? "#{identifier.system}|#{identifier.value}" : nil
+          else
+            element.value
+          end
+        when FHIR::Coding
+          if include_system
+            coding = find_a_value_at(scratch_resources_for_patient(patient_id), path) do |coding|
+              coding.code.present? && coding.system.present?
+            end
+            coding.present? ? "#{coding.system}|#{coding.code}" : nil
+          else
+            element.code
+          end
+        when FHIR::HumanName
+          element.family || element.given&.first || element.text
+        when FHIR::Address
+          element.text || element.city || element.state || element.postalCode || element.country
+        else
+          element
+        end
+      escaped_value = search_value&.gsub(',', '\\,')
+      escaped_value
+    end
+
+    def save_resource_reference(resource_type, reference)
+      scratch[:references] ||= {}
+      scratch[:references][resource_type] ||= Set.new
+      scratch[:references][resource_type] << reference
+    end
+
+    def save_delayed_references(resources, containing_resource_type = self.resource_type)
+      resources.each do |resource|
+        references_to_save(containing_resource_type).each do |reference_to_save|
+          resolve_path(resource, reference_to_save[:path])
+            .select { |reference| reference.is_a?(FHIR::Reference) && !reference.contained? }
+            .each do |reference|
+              resource_type = reference.resource_class.name.demodulize
+              need_to_save = reference_to_save[:resources].include?(resource_type)
+              next unless need_to_save
+
+              save_resource_reference(resource_type, reference)
+            end
+        end
+      end
+    end
+
+    #### RESULT CHECKING ####
+
+    def check_resource_against_params(resource, params)
+      params.each do |name, search_value|
+        path = search_param_path(name)
+        type = metadata.search_definitions[name.to_sym][:type]
+        values_found =
+          resolve_path(resource, path)
+            .map do |value|
+              if value.is_a? FHIR::Reference
+                value.reference
+              else
+                value
+              end
+            end
+
+        match_found =
+          case type
+          when 'Period', 'date', 'instant', 'dateTime'
+            values_found.any? { |date| validate_date_search(search_value, date) }
+          when 'HumanName'
+            # When a string search parameter refers to the types HumanName and Address,
+            # the search covers the elements of type string, and does not cover elements such as use and period
+            # https://www.hl7.org/fhir/search.html#string
+            search_value_downcase = search_value.downcase
+            values_found.any? do |name|
+              name&.text&.downcase&.start_with?(search_value_downcase) ||
+                name&.family&.downcase&.start_with?(search_value_downcase) ||
+                name&.given&.any? { |given| given.downcase.start_with?(search_value_downcase) } ||
+                name&.prefix&.any? { |prefix| prefix.downcase.start_with?(search_value_downcase) } ||
+                name&.suffix&.any? { |suffix| suffix.downcase.start_with?(search_value_downcase) }
+            end
+          when 'Address'
+            search_value_downcase = search_value.downcase
+            values_found.any? do |address|
+              address&.text&.downcase&.start_with?(search_value_downcase) ||
+              address&.city&.downcase&.start_with?(search_value_downcase) ||
+              address&.state&.downcase&.start_with?(search_value_downcase) ||
+              address&.postalCode&.downcase&.start_with?(search_value_downcase) ||
+              address&.country&.downcase&.start_with?(search_value_downcase)
+            end
+          when 'CodeableConcept'
+            # FHIR token search (https://www.hl7.org/fhir/search.html#token): "When in doubt, servers SHOULD 
+            # treat tokens in a case-insensitive manner, on the grounds that including undesired data has 
+            # less safety implications than excluding desired behavior". 
+            codings = values_found.flat_map(&:coding)
+            if search_value.include? '|'
+              system = search_value.split('|').first
+              code = search_value.split('|').last
+              codings&.any? { |coding| coding.system == system && coding.code&.casecmp?(code) }
+            else
+              codings&.any? { |coding| coding.code&.casecmp?(search_value) }
+            end
+          when 'Coding'
+            if search_value.include? '|'
+              system = search_value.split('|').first
+              code = search_value.split('|').last
+              values_found.any? { |coding| coding.system == system && coding.code&.casecmp?(code) }
+            else
+              values_found.any? { |coding| coding.code&.casecmp?(search_value) }
+            end
+          when 'Identifier'
+            if search_value.include? '|'
+              values_found.any? { |identifier| "#{identifier.system}|#{identifier.value}" == search_value }
+            else
+              values_found.any? { |identifier| identifier.value == search_value }
+            end
+          when 'string'
+            searched_values = search_value.downcase.split(/(?<!\\\\),/).map{ |string| string.gsub('\\,', ',') }
+            values_found.any? do |value_found|
+              searched_values.any? { |searched_value| value_found.downcase.starts_with? searched_value }
+            end
+          else
+            # searching by patient requires special case because we are searching by a resource identifier
+            # references can also be URL's, so we made need to resolve those url's
+            if ['subject', 'patient'].include? name.to_s
+              id = search_value.split('Patient/').last
+              possible_values = [id, 'Patient/' + id, "#{url}/Patient/\#{id}"]
+              values_found.any? do |reference|
+                possible_values.include? reference
+              end
+            else
+              search_values = search_value.split(/(?<!\\\\),/).map { |string| string.gsub('\\,', ',') }
+              values_found.any? { |value_found| search_values.include? value_found }
+            end
+          end
+
+        assert match_found,
+               "#{resource_type}/#{resource.id} did not match the search parameters:\n" \
+               "* Expected: #{search_value}\n" \
+               "* Found: #{values_found.map(&:inspect).join(', ')}"
+      end
+    end
+  end
+end