pacio_inferno_core 0.1.0

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data/LICENSE

@@ -0,0 +1,201 @@
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data/lib/pacio_inferno_core/custom_groups/capability_statement/conformance_support_test.rb

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+module PacioInfernoCore
+  class ConformanceSupportTest < Inferno::Test
+    id :pacio_inferno_core_conformance_support
+    title 'FHIR Server supports the conformance interaction'
+    description %(
+      The conformance 'whole system' interaction provides a method to get the
+      CapabilityStatement for the FHIR server. This test checks that the
+      server responds to a `GET` request at the following endpoint:
+
+      ```
+      GET [base]/metadata
+      ```
+
+      This test checks the following SHALL requirement:
+
+      > Applications SHALL return a resource that describes the functionality
+        of the server end-point.
+
+      [http://hl7.org/fhir/R4/http.html#capabilities](http://hl7.org/fhir/R4/http.html#capabilities)
+
+      It does this by checking that the server responds with an HTTP OK 200
+      status code and that the body of the response contains a valid
+      [CapabilityStatement
+      resource](http://hl7.org/fhir/R4/capabilitystatement.html). This test
+      does not inspect the content of the CapabilityStatement to see if it
+      contains the required information. It only checks to see if the RESTful
+      interaction is supported and returns a valid CapabilityStatement
+      resource.
+    )
+    makes_request :capability_statement
+
+    run do
+      fhir_client.set_no_auth
+      fhir_get_capability_statement(name: :capability_statement)
+
+      assert_response_status(200)
+      assert_resource_type(:capability_statement)
+      assert_valid_resource
+    end
+  end
+end

data/lib/pacio_inferno_core/custom_groups/capability_statement/fhir_version_test.rb

@@ -0,0 +1,15 @@
+module PacioInfernoCore
+  class FHIRVersionTest < Inferno::Test
+    id :pacio_inferno_core_fhir_version
+    title 'Server is using FHIR R4'
+    description %(
+        This test inspects the CapabilityStatement returned by the server to
+        verify that the server is using FHIR R4.
+      )
+
+    run do
+      server_version = fhir_client.detect_version.to_s.upcase
+      assert server_version == 'R4', "Server is using FHIR version #{server_version} rather than R4"
+    end
+  end
+end

data/lib/pacio_inferno_core/custom_groups/capability_statement/instantiate_test.rb

@@ -0,0 +1,23 @@
+module PacioInfernoCore
+  class InstantiateTest < Inferno::Test
+    id :pacio_inferno_core_instantiate
+    title 'Server instantiates US Core Server'
+    description %(
+        This test inspects the CapabilityStatement returned by the server to
+        verify that the server instantiates http://hl7.org/fhir/us/core/CapabilityStatement/us-core-server
+      )
+    uses_request :capability_statement
+
+    run do
+      assert_resource_type(:capability_statement)
+      capability_statement = resource
+
+      include_us_core = capability_statement.instantiates&.any? do |url|
+        url.split('|').first == 'http://hl7.org/fhir/us/core/CapabilityStatement/us-core-server'
+      end
+
+      assert include_us_core,
+             "Server CapabilityStatement.instantiates does not include 'http://hl7.org/fhir/us/core/CapabilityStatement/us-core-server'"
+    end
+  end
+end

data/lib/pacio_inferno_core/custom_groups/capability_statement/json_support_test.rb

@@ -0,0 +1,40 @@
+module PacioInfernoCore
+  class JSONSupportTest < Inferno::Test
+    id :pacio_inferno_core_json_support
+    title 'FHIR server capability states JSON support'
+    description %(
+      FHIR provides multiple [representation
+      formats](https://www.hl7.org/fhir/formats.html) for resources, including
+      JSON and XML. US Core profiles require servers to use the [JSON
+      representation](https://www.hl7.org/fhir/json.html):
+
+      [```The US Core Server **SHALL** Support json source formats for all US
+      Core
+      interactions.```](http://hl7.org/fhir/us/core/CapabilityStatement-us-core-server.html#behavior)
+
+      The FHIR conformance interaction require servers to describe which
+      formats are available for clients to use. The server must explicitly
+      state that JSON is supported. This is located in the [format
+      element](https://www.hl7.org/fhir/capabilitystatement-definitions.html#CapabilityStatement.format)
+      of the CapabilityStatement Resource.
+
+      This test checks that one of the following values are located in the
+      format field.
+
+      * json
+      * application/json
+      * application/fhir+json
+    )
+    uses_request :capability_statement
+
+    run do
+      assert_resource_type(:capability_statement)
+
+      json_formats = ['json', 'application/json', 'application/fhir+json']
+      server_formats = resource.format
+
+      assert server_formats.any? { |format| json_formats.include? format },
+             'CapabilityStatement does not state support for JSON'
+    end
+  end
+end

data/lib/pacio_inferno_core/date_search_validation.rb

@@ -0,0 +1,112 @@
+# frozen_string_literal: true
+
+module PacioInfernoCore
+  module DateSearchValidation
+    def get_fhir_datetime_range(datetime)
+      range = { start: DateTime.xmlschema(datetime), end: nil }
+      range[:end] =
+        if /^\d{4}$/.match?(datetime) # YYYY
+          range[:start].next_year - 1.seconds
+        elsif /^\d{4}-\d{2}$/.match?(datetime) # YYYY-MM
+          range[:start].next_month - 1.seconds
+        elsif /^\d{4}-\d{2}-\d{2}$/.match?(datetime) # YYYY-MM-DD
+          range[:start].next_day - 1.seconds
+        else # YYYY-MM-DDThh:mm:ss+zz:zz
+          range[:start]
+        end
+      range
+    end
+
+    def get_fhir_period_range(period)
+      range = { start: nil, end: nil }
+      range[:start] = DateTime.xmlschema(period.start) unless period.start.nil?
+      return range if period.end.nil?
+
+      period_end_beginning = DateTime.xmlschema(period.end)
+      range[:end] =
+        if /^\d{4}$/.match?(period.end) # YYYY
+          period_end_beginning.next_year - 1.seconds
+        elsif /^\d{4}-\d{2}$/.match?(period.end) # YYYY-MM
+          period_end_beginning.next_month - 1.seconds
+        elsif /^\d{4}-\d{2}-\d{2}$/.match?(period.end) # YYYY-MM-DD
+          period_end_beginning.next_day - 1.seconds
+        else # YYYY-MM-DDThh:mm:ss+zz:zz
+          period_end_beginning
+        end
+      range
+    end
+
+    def fhir_date_comparer(search_range, target_range, comparator, extend_start = false, extend_end = false)
+      # Implicitly, a missing lower boundary is "less than" any actual date. A missing upper boundary is "greater than" any actual date.
+      case comparator
+      when 'eq' # the range of the search value fully contains the range of the target value
+        !target_range[:start].nil? && !target_range[:end].nil? && search_range[:start] <= target_range[:start] && search_range[:end] >= target_range[:end]
+      when 'ne' # the range of the search value does not fully contain the range of the target value
+        target_range[:start].nil? || target_range[:end].nil? || search_range[:start] > target_range[:start] || search_range[:end] < target_range[:end]
+      when 'gt' #  the range above the search value intersects (i.e. overlaps) with the range of the target value
+        target_range[:end].nil? || search_range[:end] < target_range[:end] || (search_range[:end] < (target_range[:end] + 1) && extend_end)
+      when 'lt' # the range below the search value intersects (i.e. overlaps) with the range of the target value
+        target_range[:start].nil? || search_range[:start] > target_range[:start] || (search_range[:start] > (target_range[:start] - 1) && extend_start)
+      when 'ge'
+        fhir_date_comparer(search_range, target_range, 'gt', extend_start,
+                           extend_end) || fhir_date_comparer(search_range, target_range, 'eq')
+      when 'le'
+        fhir_date_comparer(search_range, target_range, 'lt', extend_start,
+                           extend_end) || fhir_date_comparer(search_range, target_range, 'eq')
+      when 'sa' # the range above the search value contains the range of the target value
+        !target_range[:start].nil? && search_range[:end] < target_range[:start]
+      when 'eb' # the range below the search value contains the range of the target value
+        !target_range[:end].nil? && search_range[:start] > target_range[:end]
+      when 'ap' # the range of the search value overlaps with the range of the target value
+        if target_range[:start].nil? || target_range[:end].nil?
+          (target_range[:start].nil? && search_range[:start] < target_range[:end]) ||
+            (target_range[:end].nil? && search_range[:end] > target_range[:start])
+        else
+          (search_range[:start] >= target_range[:start] && search_range[:start] <= target_range[:end]) ||
+            (search_range[:end] >= target_range[:start] && search_range[:end] <= target_range[:end])
+        end
+      end
+    end
+
+    def validate_date_search(search_value, target_value)
+      if target_value.instance_of? FHIR::Period
+        validate_period_search(search_value, target_value)
+      else
+        validate_datetime_search(search_value, target_value)
+      end
+    end
+
+    def validate_datetime_search(search_value, target_value)
+      comparator = search_value[0..1]
+      if %w[eq ge gt le lt ne sa eb ap].include? comparator
+        search_value = search_value[2..-1]
+      else
+        comparator = 'eq'
+      end
+      search_is_date = is_date?(search_value)
+      target_is_date = is_date?(target_value)
+      search_range = get_fhir_datetime_range(search_value)
+      target_range = get_fhir_datetime_range(target_value)
+      fhir_date_comparer(search_range, target_range, comparator, !search_is_date && target_is_date,
+                         !search_is_date && target_is_date)
+    end
+
+    def validate_period_search(search_value, target_value)
+      comparator = search_value[0..1]
+      if %w[eq ge gt le lt ne sa eb ap].include? comparator
+        search_value = search_value[2..-1]
+      else
+        comparator = 'eq'
+      end
+      search_is_date = is_date?(search_value)
+      search_range = get_fhir_datetime_range(search_value)
+      target_range = get_fhir_period_range(target_value)
+      fhir_date_comparer(search_range, target_range, comparator, !search_is_date && is_date?(target_value.start),
+                         !search_is_date && is_date?(target_value.end))
+    end
+
+    def is_date?(value)
+      /^\d{4}(-\d{2})?(-\d{2})?$/.match?(value) # YYYY or YYYY-MM or YYYY-MM-DD
+    end
+  end
+end

data/lib/pacio_inferno_core/fhir_resource_navigation.rb

@@ -0,0 +1,7 @@
+require_relative 'primitive_type'
+
+module PacioInfernoCore
+  # This functionality has been moved to Inferno Core, but this reference is
+  # retained to avoid a breaking change.
+  FHIRResourceNavigation = Inferno::DSL::FHIRResourceNavigation
+end

data/lib/pacio_inferno_core/generator/group_generator.rb

@@ -0,0 +1,161 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module PacioInfernoCore
+  class Generator
+    class GroupGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          ig_metadata.ordered_groups
+            .reject { |group| SpecialCases.exclude_group? group }
+            .each { |group| new(group, base_output_dir).generate }
+        end
+      end
+
+      attr_accessor :group_metadata, :base_output_dir
+
+      def initialize(group_metadata, base_output_dir)
+        self.group_metadata = group_metadata
+        self.base_output_dir = base_output_dir
+      end
+
+      def template
+        @template ||= File.read(File.join(__dir__, 'templates', 'group.rb.erb'))
+      end
+
+      def output
+        @output ||= ERB.new(template, trim_mode: '-').result(binding)
+      end
+
+      def naming
+        self.class.module_parent::Naming
+      end
+
+      def base_output_file_name
+        "#{class_name.underscore}.rb"
+      end
+
+      def base_metadata_file_name
+        'metadata.yml'
+      end
+
+      def class_name
+        "#{naming.upper_camel_case_for_profile(group_metadata)}Group"
+      end
+
+      def module_name_with_version
+        "#{naming.module_name}#{group_metadata.reformatted_version.upcase}"
+      end
+
+      def title
+        group_metadata.title
+      end
+
+      def short_description
+        group_metadata.short_description
+      end
+
+      def output_file_name
+        File.join(base_output_dir, base_output_file_name)
+      end
+
+      def metadata_file_name
+        File.join(base_output_dir, profile_identifier, base_metadata_file_name)
+      end
+
+      def profile_identifier
+        naming.snake_case_for_profile(group_metadata)
+      end
+
+      def group_id
+        "#{naming.prefix}_#{group_metadata.reformatted_version}_#{profile_identifier}"
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def search_validation_resource_type
+        "#{resource_type} resources"
+      end
+
+      def profile_name
+        group_metadata.profile_name
+      end
+
+      def profile_url
+        group_metadata.profile_url
+      end
+
+      def optional?
+        SpecialCases::OPTIONAL_RESOURCES.include?(resource_type) || group_metadata.optional_profile?
+      end
+
+      def generate
+        add_special_tests
+        File.write(output_file_name, output)
+        group_metadata.id = group_id
+        group_metadata.file_name = base_output_file_name
+        File.write(metadata_file_name, YAML.dump(group_metadata.to_hash))
+      end
+
+      def add_special_tests; end
+
+      def test_id_list
+        @test_id_list ||=
+          group_metadata.tests.map { |test| test[:id] }
+      end
+
+      def test_file_list
+        @test_file_list ||=
+          group_metadata.tests.map do |test|
+            name_without_suffix = test[:file_name].delete_suffix('.rb')
+            name_without_suffix.start_with?('..') ? name_without_suffix : "#{profile_identifier}/#{name_without_suffix}"
+          end
+      end
+
+      def required_searches
+        group_metadata.searches.select { |search| search[:expectation] == 'SHALL' }
+      end
+
+      def search_param_name_string
+        required_searches
+          .map { |search| search[:names].join(' + ') }
+          .map { |names| "* #{names}" }
+          .join("\n")
+      end
+
+      def search_description
+        return '' if required_searches.blank?
+
+        <<~SEARCH_DESCRIPTION
+          ## Searching
+          This test sequence will first perform each required search associated
+          with this resource. This sequence will perform searches with the
+          following parameters:
+
+          #{search_param_name_string}
+
+          ### Search Parameters
+          The first search uses the selected patient(s) from the prior launch
+          sequence. Any subsequent searches will look for its parameter values
+          from the results of the first search. For example, the `identifier`
+          search in the patient sequence is performed by looking for an existing
+          `Patient.identifier` from any of the resources returned in the `_id`
+          search. If a value cannot be found this way, the search is skipped.
+
+          ### Search Validation
+          Inferno will retrieve up to the first 20 bundle pages of the reply for
+          #{search_validation_resource_type} and save them for subsequent tests. Each of
+          these resources is then checked to see if it matches the searched
+          parameters in accordance with [FHIR search
+          guidelines](https://www.hl7.org/fhir/search.html). The test will fail,
+          for example, if a Patient search for `gender=male` returns a `female`
+          patient.
+        SEARCH_DESCRIPTION
+      end
+
+      def description; end
+    end
+  end
+end