inferno_core 0.0.8.pre2 → 0.1.1.pre
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- checksums.yaml +4 -4
- data/lib/inferno/apps/web/controllers/test_runs/create.rb +2 -1
- data/lib/inferno/apps/web/serializers/result.rb +1 -0
- data/lib/inferno/apps/web/serializers/test.rb +4 -0
- data/lib/inferno/apps/web/serializers/test_group.rb +4 -0
- data/lib/inferno/apps/web/serializers/test_suite.rb +3 -0
- data/lib/inferno/db/migrations/001_create_initial_structure.rb +54 -53
- data/lib/inferno/db/migrations/002_add_wait_support.rb +2 -2
- data/lib/inferno/db/migrations/003_update_session_data.rb +7 -7
- data/lib/inferno/db/migrations/004_add_request_results_table.rb +2 -2
- data/lib/inferno/db/migrations/005_add_updated_at_index_to_results.rb +1 -1
- data/lib/inferno/db/migrations/006_remove_unused_tables.rb +38 -0
- data/lib/inferno/db/schema.rb +17 -43
- data/lib/inferno/dsl/configurable.rb +12 -5
- data/lib/inferno/dsl/fhir_client.rb +58 -6
- data/lib/inferno/dsl/fhir_client_builder.rb +16 -0
- data/lib/inferno/dsl/http_client.rb +62 -0
- data/lib/inferno/dsl/oauth_credentials.rb +119 -0
- data/lib/inferno/dsl/runnable.rb +87 -9
- data/lib/inferno/entities/has_runnable.rb +26 -0
- data/lib/inferno/entities/request.rb +7 -1
- data/lib/inferno/entities/result.rb +8 -4
- data/lib/inferno/entities/test_group.rb +4 -6
- data/lib/inferno/entities/test_run.rb +1 -18
- data/lib/inferno/entities/test_suite.rb +3 -4
- data/lib/inferno/entities.rb +1 -0
- data/lib/inferno/exceptions.rb +19 -0
- data/lib/inferno/ext/fhir_client.rb +13 -0
- data/lib/inferno/public/bundle.js +15 -15
- data/lib/inferno/repositories/session_data.rb +40 -6
- data/lib/inferno/result_summarizer.rb +40 -0
- data/lib/inferno/spec_support.rb +1 -1
- data/lib/inferno/test_runner.rb +13 -9
- data/lib/inferno/version.rb +1 -1
- data/spec/factories/request.rb +1 -1
- data/spec/factories/result.rb +2 -2
- data/spec/fixtures/basic_test_group.rb +1 -0
- metadata +7 -2
@@ -103,6 +103,68 @@ module Inferno
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end
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end
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# Perform an HTTP DELETE request
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#
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# @param url [String] if this request is using a defined client, this will
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# be appended to the client's url. Must be an absolute url for requests
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# made without a defined client
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# @param client [Symbol]
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# @param name [Symbol] Name for this request to allow it to be used by
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# other tests
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# @return [Inferno::Entities::Request]
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def delete(url = '', client: :default, name: :nil, **options)
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store_request('outgoing', name) do
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client = http_client(client)
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if client
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client.delete(url, nil, options[:headers])
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elsif url.match?(%r{\Ahttps?://})
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Faraday.delete(url, nil, options[:headers])
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else
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raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
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end
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end
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end
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# Perform an HTTP GET request and stream the response
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#
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# @param block [Proc] A Proc object whose input will be the string chunks
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# received while streaming response to the get request.
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# @param url [String] If this request is using a defined client, this will
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# be appended to the client's url. Must be an absolute url for requests
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# made without a defined client
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# @param limit [Integer] The number of streamed-in chunks to be stored in
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# the response body. This optional input defaults to 100.
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# @param client [Symbol]
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# @param name [Symbol] Name for this request to allow it to be used by
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# other tests
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# @option options [Hash] Input headers here - headers are optional and
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# must be entered as the last piece of input to this method
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# @return [Inferno::Entities::Request]
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def stream(block, url = '', limit = 100, client: :default, name: nil, **options)
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streamed = []
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collector = proc do |chunk, bytes|
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streamed << chunk if limit.positive?
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limit -= 1
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block.call(chunk, bytes)
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end
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store_request('outgoing', name) do
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client = http_client(client)
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if client
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response = client.get(url, nil, options[:headers]) { |req| req.options.on_data = collector }
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elsif url.match?(%r{\Ahttps?://})
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response = Faraday.get(url, nil, options[:headers]) { |req| req.options.on_data = collector }
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else
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raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
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end
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response.env.body = streamed.join
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response
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end
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end
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module ClassMethods
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# @private
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def http_client_definitions
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@@ -0,0 +1,119 @@
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require_relative '../entities/attributes'
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module Inferno
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module DSL
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class OAuthCredentials
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ATTRIBUTES = [
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:access_token,
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:refresh_token,
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:token_url,
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:client_id,
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:client_secret,
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:token_retrieval_time,
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:expires_in,
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:name
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].freeze
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include Entities::Attributes
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attr_accessor :client
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def initialize(raw_attributes_hash)
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attributes_hash = raw_attributes_hash.symbolize_keys
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invalid_keys = attributes_hash.keys - ATTRIBUTES
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raise Exceptions::UnknownAttributeException.new(invalid_keys, self.class) if invalid_keys.present?
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attributes_hash.each do |name, value|
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value = DateTime.parse(value) if name == :token_retrieval_time && value.is_a?(String)
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instance_variable_set(:"@#{name}", value)
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end
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self.token_retrieval_time = DateTime.now if token_retrieval_time.blank?
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end
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# @api private
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def to_hash
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self.class::ATTRIBUTES.each_with_object({}) do |attribute, hash|
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value = send(attribute)
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next if value.nil?
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value = token_retrieval_time.iso8601 if attribute == :token_retrieval_time
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hash[attribute] = value
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end
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end
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# @api private
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def to_s
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JSON.generate(to_hash)
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end
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# @api private
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def add_to_client(client)
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client.oauth_credentials = self
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self.client = client
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return unless access_token.present?
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client.set_bearer_token(access_token)
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end
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# @api private
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def need_to_refresh?
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return false if access_token.blank? || refresh_token.blank?
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return true if expires_in.blank?
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token_retrieval_time.to_i + expires_in - DateTime.now.to_i < 60
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end
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# @api private
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def able_to_refresh?
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refresh_token.present? && token_url.present?
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end
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# @api private
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def confidential_client?
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client_id.present? && client_secret.present?
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end
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# @api private
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def oauth2_refresh_params
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{
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'grant_type' => 'refresh_token',
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'refresh_token' => refresh_token
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}
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end
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# @api private
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def oauth2_refresh_headers
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base_headers = { 'Content-Type' => 'application/x-www-form-urlencoded' }
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return base_headers unless confidential_client?
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credentials = "#{client_id}:#{client_secret}"
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base_headers.merge(
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'Authorization' => "Basic #{Base64.strict_encode64(credentials)}"
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)
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end
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def update_from_response_body(request)
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token_response_body = JSON.parse(request.response_body)
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expires_in = token_response_body['expires_in'].is_a?(Numeric) ? token_response_body['expires_in'] : nil
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self.access_token = token_response_body['access_token']
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self.refresh_token = token_response_body['refresh_token']
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self.expires_in = expires_in
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self.token_retrieval_time = DateTime.now
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add_to_client(client)
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self
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end
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end
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end
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end
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data/lib/inferno/dsl/runnable.rb
CHANGED
@@ -85,7 +85,6 @@ module Inferno
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klass.parent = self
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-
child_metadata[:collection] << klass
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children << klass
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configure_child_class(klass, hash_args)
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@@ -164,6 +163,8 @@ module Inferno
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klass.config(config)
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klass.children.select!(&:required?) if hash_args.delete(:exclude_optional)
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hash_args.each do |key, value|
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if value.is_a? Array
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klass.send(key, *value)
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@@ -212,6 +213,16 @@ module Inferno
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@title = new_title
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end
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# Set/Get a runnable's short title
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#
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# @param new_short_title [String]
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# @return [String] the short title
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def short_title(new_short_title = nil)
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return @short_title if new_short_title.nil?
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@short_title = new_short_title
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end
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# Set/Get a runnable's description
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#
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# @param new_description [String]
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@@ -222,6 +233,26 @@ module Inferno
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@description = format_markdown(new_description)
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end
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# Set/Get a runnable's short one-sentence description
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#
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# @param new_short_description [String]
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# @return [String] the one-sentence description
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def short_description(new_short_description = nil)
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return @short_description if new_short_description.nil?
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@short_description = format_markdown(new_short_description)
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end
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# Set/Get a runnable's input instructions
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#
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# @param new_input_instructions [String]
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# @return [String] the input instructions
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def input_instructions(new_input_instructions = nil)
|
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return @input_instructions if new_input_instructions.nil?
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@input_instructions = format_markdown(new_input_instructions)
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end
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# Define inputs
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#
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# @param identifier [Symbol] identifier for the input
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@@ -229,12 +260,14 @@ module Inferno
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# @param input_definition [Hash] options for input such as type, description, or title
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# @option input_definition [String] :title Human readable title for input
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# @option input_definition [String] :description Description for the input
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-
# @option input_definition [String] :type text | textarea
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# @option input_definition [String] :type text | textarea | radio
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# @option input_definition [String] :default The default value for the input
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# @option input_definition [Boolean] :optional Set to true to not require input for test execution
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# @option input_definition [Hash] :options Possible input option formats based on input type
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# @option options [Array] :list_options Array of options for input formats that require a list of possible values
|
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# @return [void]
|
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# @example
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-
# input :
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# input :patient_id, title: 'Patient ID', description: 'The ID of the patient being searched for',
|
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# default: 'default_patient_id'
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# @example
|
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# input :textarea, title: 'Textarea Input Example', type: 'textarea', optional: true
|
@@ -250,16 +283,60 @@ module Inferno
|
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end
|
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end
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# Mark as optional. Tests are required by default.
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#
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# @param optional [Boolean]
|
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# @return [void]
|
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#
|
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def optional(optional = true) # rubocop:disable Style/OptionalBooleanParameter
|
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@optional = optional
|
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+
end
|
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|
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# Mark as required
|
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#
|
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# Tests are required by default. This method is provided to make an
|
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# existing optional test required.
|
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#
|
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# @param required[Boolean]
|
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# @return [void]
|
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def required(required = true) # rubocop:disable Style/OptionalBooleanParameter
|
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@optional = !required
|
304
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end
|
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|
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# The test or group is optional if true
|
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#
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# @return [Boolean]
|
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def optional?
|
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!!@optional
|
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end
|
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+
|
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# The test or group is required if true
|
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#
|
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# @return [Boolean]
|
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+
def required?
|
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!optional?
|
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+
end
|
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+
|
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# Define outputs
|
254
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#
|
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-
# @param
|
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+
# @param identifier [Symbol] identifier for the output
|
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# @param other_identifiers [Symbol] array of symbols if specifying multiple outputs
|
324
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# @param output_definition [Hash] options for output
|
325
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+
# @option output_definition [String] :type text | textarea | oauth_credentials
|
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|
# @return [void]
|
257
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|
# @example
|
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-
# output :patient_id, :
|
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-
|
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-
|
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|
-
|
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-
|
328
|
+
# output :patient_id, :condition_id, :observation_id
|
329
|
+
# @example
|
330
|
+
# output :oauth_credentials, type: 'oauth_credentials'
|
331
|
+
def output(identifier, *other_identifiers, **output_definition)
|
332
|
+
if other_identifiers.present?
|
333
|
+
[identifier, *other_identifiers].compact.each do |output_identifier|
|
334
|
+
outputs << output_identifier
|
335
|
+
config.add_output(output_identifier)
|
336
|
+
end
|
337
|
+
else
|
338
|
+
outputs << identifier
|
339
|
+
config.add_output(identifier, output_definition)
|
263
340
|
end
|
264
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|
end
|
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|
@@ -395,6 +472,7 @@ module Inferno
|
|
395
472
|
required_inputs.map(&:to_s) - submitted_inputs.map { |input| input[:name] }
|
396
473
|
end
|
397
474
|
|
475
|
+
# @private
|
398
476
|
def user_runnable?
|
399
477
|
@user_runnable ||= parent.nil? ||
|
400
478
|
!parent.respond_to?(:run_as_group?) ||
|
@@ -0,0 +1,26 @@
|
|
1
|
+
module Inferno
|
2
|
+
module Entities
|
3
|
+
module HasRunnable
|
4
|
+
# Returns the Test, TestGroup, or TestSuite associated with this entity
|
5
|
+
#
|
6
|
+
# @return [Inferno::Entities::Test, Inferno::Entities::TestGroup, Inferno::Entities::TestSuite]
|
7
|
+
def runnable
|
8
|
+
return @runnable if @runnable
|
9
|
+
|
10
|
+
@runnable = (test || test_group || test_suite || load_runnable)
|
11
|
+
end
|
12
|
+
|
13
|
+
private
|
14
|
+
|
15
|
+
def load_runnable
|
16
|
+
if test_id.present?
|
17
|
+
@test = Inferno::Repositories::Tests.new.find(test_id)
|
18
|
+
elsif test_group_id.present?
|
19
|
+
@test_group = Inferno::Repositories::TestGroups.new.find(test_group_id)
|
20
|
+
elsif test_suite_id.present?
|
21
|
+
@test_suite = Inferno::Repositories::TestSuites.new.find(test_suite_id)
|
22
|
+
end
|
23
|
+
end
|
24
|
+
end
|
25
|
+
end
|
26
|
+
end
|
@@ -186,6 +186,12 @@ module Inferno
|
|
186
186
|
.map { |header_name, value| Header.new(name: header_name.downcase, value: value, type: 'request') }
|
187
187
|
response_headers = response[:headers]
|
188
188
|
.map { |header_name, value| Header.new(name: header_name.downcase, value: value, type: 'response') }
|
189
|
+
request_body =
|
190
|
+
if request.dig(:headers, 'Content-Type')&.include?('application/x-www-form-urlencoded')
|
191
|
+
URI.encode_www_form(request[:payload])
|
192
|
+
else
|
193
|
+
request[:payload]
|
194
|
+
end
|
189
195
|
|
190
196
|
new(
|
191
197
|
verb: request[:method],
|
@@ -193,7 +199,7 @@ module Inferno
|
|
193
199
|
direction: direction,
|
194
200
|
name: name,
|
195
201
|
status: response[:code].to_i,
|
196
|
-
request_body:
|
202
|
+
request_body: request_body,
|
197
203
|
response_body: response[:body],
|
198
204
|
test_session_id: test_session_id,
|
199
205
|
headers: request_headers + response_headers
|
@@ -47,9 +47,10 @@ module Inferno
|
|
47
47
|
:test_session_id, :result, :result_message, :messages, :requests,
|
48
48
|
:input_json, :output_json
|
49
49
|
].freeze
|
50
|
-
RESULT_OPTIONS = ['cancel', 'wait', 'running', 'error', 'fail', 'skip', '
|
50
|
+
RESULT_OPTIONS = ['cancel', 'wait', 'running', 'error', 'fail', 'skip', 'pass', 'omit'].freeze
|
51
51
|
|
52
52
|
include Inferno::Entities::Attributes
|
53
|
+
include Inferno::Entities::HasRunnable
|
53
54
|
|
54
55
|
def initialize(params)
|
55
56
|
super(params, ATTRIBUTES - [:messages, :requests])
|
@@ -58,9 +59,12 @@ module Inferno
|
|
58
59
|
@requests = (params[:requests] || []).map { |request| Request.new(request) }
|
59
60
|
end
|
60
61
|
|
61
|
-
|
62
|
-
|
63
|
-
|
62
|
+
def optional?
|
63
|
+
runnable.optional?
|
64
|
+
end
|
65
|
+
|
66
|
+
def required?
|
67
|
+
!optional?
|
64
68
|
end
|
65
69
|
|
66
70
|
# @return [Boolean]
|
@@ -32,11 +32,11 @@ module Inferno
|
|
32
32
|
end
|
33
33
|
|
34
34
|
def groups
|
35
|
-
|
35
|
+
children.select { |child| child < Inferno::Entities::TestGroup }
|
36
36
|
end
|
37
37
|
|
38
38
|
def tests
|
39
|
-
|
39
|
+
children.select { |child| child < Inferno::Entities::Test }
|
40
40
|
end
|
41
41
|
|
42
42
|
# Methods to configure Inferno::DSL::Runnable
|
@@ -54,16 +54,14 @@ module Inferno
|
|
54
54
|
def group_metadata
|
55
55
|
{
|
56
56
|
class: TestGroup,
|
57
|
-
repo: repository
|
58
|
-
collection: groups
|
57
|
+
repo: repository
|
59
58
|
}
|
60
59
|
end
|
61
60
|
|
62
61
|
def test_metadata
|
63
62
|
{
|
64
63
|
class: Test,
|
65
|
-
repo: Inferno::Repositories::Tests.new
|
66
|
-
collection: tests
|
64
|
+
repo: Inferno::Repositories::Tests.new
|
67
65
|
}
|
68
66
|
end
|
69
67
|
|
@@ -52,6 +52,7 @@ module Inferno
|
|
52
52
|
].freeze
|
53
53
|
|
54
54
|
include Inferno::Entities::Attributes
|
55
|
+
include Inferno::Entities::HasRunnable
|
55
56
|
|
56
57
|
attr_accessor :test_session
|
57
58
|
|
@@ -63,12 +64,6 @@ module Inferno
|
|
63
64
|
@test_session = params[:test_session]
|
64
65
|
end
|
65
66
|
|
66
|
-
def runnable
|
67
|
-
return @runnable if @runnable
|
68
|
-
|
69
|
-
@runnable = (test || test_group || test_suite || load_runnable)
|
70
|
-
end
|
71
|
-
|
72
67
|
def to_hash
|
73
68
|
super.merge(test_session: test_session).compact
|
74
69
|
end
|
@@ -76,18 +71,6 @@ module Inferno
|
|
76
71
|
def test_count
|
77
72
|
@test_count ||= runnable.test_count
|
78
73
|
end
|
79
|
-
|
80
|
-
private
|
81
|
-
|
82
|
-
def load_runnable
|
83
|
-
if test_id.present?
|
84
|
-
@test = Inferno::Repositories::Tests.new.find(test_id)
|
85
|
-
elsif test_group_id.present?
|
86
|
-
@test_group = Inferno::Repositories::TestGroups.new.find(test_group_id)
|
87
|
-
elsif test_suite_id.present?
|
88
|
-
@test_suite = Inferno::Repositories::TestSuites.new.find(test_suite_id)
|
89
|
-
end
|
90
|
-
end
|
91
74
|
end
|
92
75
|
end
|
93
76
|
end
|
@@ -22,7 +22,7 @@ module Inferno
|
|
22
22
|
return @default_group if @default_group
|
23
23
|
|
24
24
|
@default_group = Class.new(TestGroup)
|
25
|
-
|
25
|
+
children << @default_group
|
26
26
|
@default_group
|
27
27
|
end
|
28
28
|
|
@@ -31,7 +31,7 @@ module Inferno
|
|
31
31
|
end
|
32
32
|
|
33
33
|
def groups
|
34
|
-
|
34
|
+
children.select { |child| child < Inferno::Entities::TestGroup }
|
35
35
|
end
|
36
36
|
|
37
37
|
# Methods to configure Inferno::DSL::Runnable
|
@@ -44,8 +44,7 @@ module Inferno
|
|
44
44
|
def group_metadata
|
45
45
|
{
|
46
46
|
class: TestGroup,
|
47
|
-
repo: Inferno::Repositories::TestGroups.new
|
48
|
-
collection: groups
|
47
|
+
repo: Inferno::Repositories::TestGroups.new
|
49
48
|
}
|
50
49
|
end
|
51
50
|
|
data/lib/inferno/entities.rb
CHANGED
data/lib/inferno/exceptions.rb
CHANGED
@@ -62,5 +62,24 @@ module Inferno
|
|
62
62
|
super('The chosen runnable must be run as part of a group')
|
63
63
|
end
|
64
64
|
end
|
65
|
+
|
66
|
+
class UnknownAttributeException < RuntimeError
|
67
|
+
def initialize(attributes, klass)
|
68
|
+
attributes_string = attributes.map { |attribute| "'#{attribute}'" }.join(', ')
|
69
|
+
super("Unknown attributes for #{klass.name}: #{attributes_string}")
|
70
|
+
end
|
71
|
+
end
|
72
|
+
|
73
|
+
class UnknownSessionDataType < RuntimeError
|
74
|
+
def initialize(output)
|
75
|
+
super("Unknown type '#{output[:type]}' for '#{output[:name]}'.")
|
76
|
+
end
|
77
|
+
end
|
78
|
+
|
79
|
+
class BadSessionDataType < RuntimeError
|
80
|
+
def initialize(name, expected_class, actual_class)
|
81
|
+
super("Expected '#{name}' to be a #{expected_class.name}, but found a #{actual_class.name}.")
|
82
|
+
end
|
83
|
+
end
|
65
84
|
end
|
66
85
|
end
|