inferno_core 1.4.3 → 1.4.5

data/lib/inferno/test_runner.rb

@@ -122,9 +122,13 @@ module Inferno
     end
 
     def check_inputs(test, _test_instance, inputs)
+      available_inputs = test.available_inputs(test_session.suite_options)
+      input_values = inputs.transform_keys { |input_identifier| test.config.input_name(input_identifier).to_s }
+
       inputs.each do |key, value|
         optional = test.config.input_optional?(key)
-        if value.nil? && !optional
+        input = available_inputs[test.config.input_name(key).to_sym]
+        if value.nil? && !optional && input.enabled?(input_values, available_inputs)
           raise Exceptions::SkipException,
                 "Input '#{test.config.input_name(key)}' is nil, skipping test."
         end

data/lib/inferno/utils/execution_script_runner.rb

@@ -3,7 +3,11 @@ require 'open3'
 module Inferno
   module Utils
     module ExecutionScriptRunner
-      def self.run_all(pattern: 'execution_scripts/**/*.yaml', inferno_base_url: nil, allow_known_errors: false)
+      def self.run_all(pattern: 'execution_scripts/**/*.yaml', inferno_base_url: nil,
+                       allow_known_errors: false, allow_commands: false,
+                       compare_messages: true, compare_result_message: true,
+                       poll_interval: 3, default_poll_timeout: 120,
+                       only_different_messages: true)
         scripts = Dir.glob(pattern)
 
         if scripts.empty?
@@ -22,7 +26,10 @@ module Inferno
             next
           end
 
-          result = run_script(config, inferno_base_url:, allow_known_errors:)
+          result = run_script(config, inferno_base_url:, allow_known_errors:, allow_commands:,
+                                      compare_messages:, compare_result_message:,
+                                      poll_interval:, default_poll_timeout:,
+                                      only_different_messages:)
           (result == :pass ? passed : failed) << config
 
           puts
@@ -31,19 +38,61 @@ module Inferno
         print_summary(passed, failed)
       end
 
-      def self.run_script(config, inferno_base_url:, allow_known_errors:)
+      def self.run_script(config, inferno_base_url:, allow_known_errors:, allow_commands: false,
+                          compare_messages: true, compare_result_message: true,
+                          poll_interval: 3, default_poll_timeout: 120,
+                          only_different_messages: true)
         puts '=' * 60
         puts "Running: #{config}"
         puts '=' * 60
 
-        allow_commands = File.basename(config, '.yaml').include?('_with_commands')
+        allow_commands ||= File.basename(config, '.yaml').include?('_with_commands')
+        cmd = build_command(config, inferno_base_url:, allow_commands:, compare_messages:,
+                                    compare_result_message:, poll_interval:, default_poll_timeout:,
+                                    only_different_messages:)
+        output, exitstatus = stream_command(*cmd)
+
+        determine_result(config, exitstatus, output, allow_known_errors)
+      end
+
+      # @private
+      def self.build_command(config, inferno_base_url:, allow_commands:, compare_messages:,
+                             compare_result_message:, poll_interval:, default_poll_timeout:,
+                             only_different_messages:)
         cmd = ['bundle', 'exec', 'inferno', 'execute_script', config]
         cmd += ['--inferno-base-url', inferno_base_url] if inferno_base_url
         cmd += ['--allow-commands'] if allow_commands
-        output, status = Open3.capture2e(*cmd)
-        puts output
+        cmd += ['--poll-interval', poll_interval.to_s] if poll_interval != 3
+        cmd += ['--default-poll-timeout', default_poll_timeout.to_s] if default_poll_timeout != 120
+        cmd + comparison_flags(compare_messages:, compare_result_message:, only_different_messages:)
+      end
+
+      # @private
+      def self.comparison_flags(compare_messages:, compare_result_message:, only_different_messages:)
+        flags = []
+        flags << '--no-compare-messages' unless compare_messages
+        flags << '--no-compare-result-message' unless compare_result_message
+        flags << '--no-only-different-messages' unless only_different_messages
+        flags
+      end
+
+      # Runs +cmd+ as a subprocess, echoing its combined stdout/stderr to the console
+      # line-by-line as it's produced (rather than buffering until the process exits),
+      # while still returning the full captured output for result determination.
+      def self.stream_command(*cmd)
+        output = +''
+        exitstatus = nil
+
+        Open3.popen2e(*cmd) do |stdin, stdout_and_stderr, wait_thread|
+          stdin.close
+          stdout_and_stderr.each_line do |line|
+            puts line
+            output << line
+          end
+          exitstatus = wait_thread.value.exitstatus
+        end
 
-        determine_result(config, status.exitstatus, output, allow_known_errors)
+        [output, exitstatus]
       end
 
       def self.determine_result(config, return_code, output, allow_known_errors)

data/lib/inferno/version.rb

@@ -1,4 +1,4 @@
 module Inferno
   # Standard patterns for gem versions: https://guides.rubygems.org/patterns/
-  VERSION = '1.4.3'.freeze
+  VERSION = '1.4.5'.freeze
 end

data/spec/spec_helper.rb

@@ -128,6 +128,24 @@ RSpec.configure do |config|
     DatabaseCleaner.cleaning { example.run }
   end
 
+  # Inferno::Entities::Test/TestGroup/TestSuite are meant to be used only as
+  # abstract bases -- real tests/groups/suites are always DSL-defined subclasses.
+  # Some specs instantiate the bare classes directly (e.g. `Inferno::Test.new`) as
+  # lightweight doubles. If anything then reads `.id` on one of those, `Runnable#id`
+  # permanently memoizes @id/@base_id/@database_id onto that *shared* class object
+  # (since it's a genuinely named Ruby class, `default_id` returns its `Module#name`).
+  # Left in place, that id leaks into every subsequently-defined anonymous subclass
+  # via `copy_instance_variables`, causing DuplicateEntityIdException collisions in
+  # unrelated, later-running examples. Reset it after every example so it can never
+  # survive to pollute a different example.
+  config.after do
+    [Inferno::Entities::Test, Inferno::Entities::TestGroup, Inferno::Entities::TestSuite].each do |klass|
+      klass.instance_variable_set(:@id, nil)
+      klass.instance_variable_set(:@base_id, nil)
+      klass.instance_variable_set(:@database_id, nil)
+    end
+  end
+
   config.include FactoryBot::Syntax::Methods
 
   config.before(:suite) do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: inferno_core
 version: !ruby/object:Gem::Version
-  version: 1.4.3
+  version: 1.4.5
 platform: ruby
 authors:
 - Stephen MacVicar
@@ -10,7 +10,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2026-08-26 00:00:00.000000000 Z
+date: 2026-10-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -556,7 +556,7 @@ files:
 - lib/inferno/apps/cli/templates/docs/_Sidebar.md
 - lib/inferno/apps/cli/templates/execution_scripts/%library_name%_script.yaml.tt
 - lib/inferno/apps/cli/templates/execution_scripts/%library_name%_script_expected.json.tt
-- lib/inferno/apps/cli/templates/execution_scripts/README.md.tt
+- lib/inferno/apps/cli/templates/execution_scripts/README.md
 - lib/inferno/apps/cli/templates/lib/%library_name%.rb.tt
 - lib/inferno/apps/cli/templates/lib/%library_name%/example_suite.rb.tt
 - lib/inferno/apps/cli/templates/lib/%library_name%/example_suite/patient_group.rb.tt
@@ -564,9 +564,11 @@ files:
 - lib/inferno/apps/cli/templates/lib/%library_name%/igs/README.md
 - lib/inferno/apps/cli/templates/lib/%library_name%/igs/put_ig_package_dot_tgz_here
 - lib/inferno/apps/cli/templates/lib/%library_name%/metadata.rb.tt
+- lib/inferno/apps/cli/templates/lib/%library_name%/requirements/%library_name%_requirements.csv
 - lib/inferno/apps/cli/templates/lib/%library_name%/requirements/Inferno Requirements
   Template.xlsx
-- lib/inferno/apps/cli/templates/lib/%library_name%/suite.rb.tt
+- lib/inferno/apps/cli/templates/lib/%library_name%/requirements/README.md
+- lib/inferno/apps/cli/templates/lib/%library_name%/requirements/generated/%test_suite_id%_requirements_coverage.csv.tt
 - lib/inferno/apps/cli/templates/lib/%library_name%/version.rb.tt
 - lib/inferno/apps/cli/templates/run.sh
 - lib/inferno/apps/cli/templates/setup.sh

data/lib/inferno/apps/cli/templates/lib/%library_name%/suite.rb.tt

@@ -1,59 +0,0 @@
-require_relative 'metadata'
-require_relative 'patient_group'
-
-module <%= module_name %>
-  class Suite < Inferno::TestSuite
-    id :<%= test_suite_id %>
-    title '<%= title_name %> Test Suite'
-    description '<%= human_name %> test suite.'
-
-    # These inputs will be available to all tests in this suite
-    input :url,
-          title: 'FHIR Server Base Url'
-
-    input :credentials,
-          title: 'OAuth Credentials',
-          type: :auth_info,
-          optional: true
-
-    # All FHIR requests in this suite will use this FHIR client
-    fhir_client do
-      url :url
-      auth_info :credentials
-    end
-
-    # All FHIR validation requests will use this FHIR validator
-    fhir_resource_validator do
-      # igs 'identifier#version' # Use this method for published IGs/versions
-      # igs 'igs/filename.tgz'   # Use this otherwise
-
-      exclude_message do |message|
-        message.message.match?(/\A\S+: \S+: URL value '.*' does not resolve/)
-      end
-    end
-
-    # Tests and TestGroups can be defined inline
-    group do
-      id :capability_statement
-      title 'Capability Statement'
-      description 'Verify that the server has a CapabilityStatement'
-
-      test do
-        id :capability_statement_read
-        title 'Read CapabilityStatement'
-        description 'Read CapabilityStatement from /metadata endpoint'
-
-        run do
-          fhir_get_capability_statement
-
-          assert_response_status(200)
-          assert_resource_type(:capability_statement)
-        end
-      end
-    end
-
-    # Tests and TestGroups can be written in separate files and then included
-    # using their id
-    group from: :patient_group
-  end
-end