From 9f23ba946f6df4ea88f89b74c38c5b0610beddac Mon Sep 17 00:00:00 2001 From: Dylan Hall Date: Thu, 23 May 2024 08:30:24 -0400 Subject: [PATCH] FI-2429: Migrate to HL7 validator wrapper (#6) * FI-2429: Migrate to HL7 validator wrapper * Add README to igs folder --- .env.development | 2 +- .env.production | 2 +- .env.test | 2 +- Gemfile.lock | 17 ++++--- config/nginx.background.conf | 47 +++++++++++------ config/nginx.conf | 50 ++++++++++++------- docker-compose.background.yml | 35 ++++++++----- docker-compose.yml | 19 ++++--- .../v1.1.0/davinci_plan_net_test_suite.rb | 10 ++-- .../generator/suite_generator.rb | 5 +- .../generator/templates/suite.rb.erb | 10 ++-- lib/davinci_plan_net_test_kit/igs/README.md | 21 ++++++++ .../reference_resolution_test.rb | 3 +- 13 files changed, 150 insertions(+), 73 deletions(-) create mode 100644 lib/davinci_plan_net_test_kit/igs/README.md diff --git a/.env.development b/.env.development index 82d40af..e8690f6 100644 --- a/.env.development +++ b/.env.development @@ -1,2 +1,2 @@ -V110_VALIDATOR_URL=http://localhost/validatorapi +FHIR_RESOURCE_VALIDATOR_URL=http://localhost/hl7validatorapi REDIS_URL=redis://localhost:6379/0 \ No newline at end of file diff --git a/.env.production b/.env.production index c260c43..719b168 100644 --- a/.env.production +++ b/.env.production @@ -1,2 +1,2 @@ REDIS_URL=redis://redis:6379/0 -V110_VALIDATOR_URL=http://validator_service:4567 \ No newline at end of file +FHIR_RESOURCE_VALIDATOR_URL=http://hl7_validator_service:3500 \ No newline at end of file diff --git a/.env.test b/.env.test index 9e95769..1545bfc 100644 --- a/.env.test +++ b/.env.test @@ -1,2 +1,2 @@ -VALIDATOR_URL=https://example.com/validatorapi +FHIR_RESOURCE_VALIDATOR_URL=https://example.com/validatorapi ASYNC_JOBS=false diff --git a/Gemfile.lock b/Gemfile.lock index fff9a36..a221316 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -146,7 +146,7 @@ GEM i18n (1.14.4) concurrent-ruby (~> 1.0) ice_nine (0.11.2) - inferno_core (0.4.33) + inferno_core (0.4.35) activesupport (~> 6.1.7.5) base62-rb (= 0.3.1) blueprinter (= 0.25.2) @@ -180,14 +180,15 @@ GEM base64 kramdown (2.4.0) rexml - method_source (1.0.0) + method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) mime-types-data (3.2024.0305) - mini_portile2 (2.8.5) + mini_portile2 (2.8.6) minitest (5.22.3) multi_json (1.15.0) - multi_xml (0.6.0) + multi_xml (0.7.1) + bigdecimal (~> 3.1) multipart-post (2.4.0) mustermann (1.1.2) ruby2_keywords (~> 0.0.1) @@ -196,14 +197,14 @@ GEM mustermann (= 1.1.2) netrc (0.11.0) nio4r (2.7.1) - nokogiri (1.16.3) + nokogiri (1.16.4) mini_portile2 (~> 2.8.2) racc (~> 1.4) - nokogiri (1.16.3-arm64-darwin) + nokogiri (1.16.4-arm64-darwin) racc (~> 1.4) - nokogiri (1.16.3-x86_64-darwin) + nokogiri (1.16.4-x86_64-darwin) racc (~> 1.4) - nokogiri (1.16.3-x86_64-linux) + nokogiri (1.16.4-x86_64-linux) racc (~> 1.4) oauth2 (1.4.11) faraday (>= 0.17.3, < 3.0) diff --git a/config/nginx.background.conf b/config/nginx.background.conf index f897472..5cacd0b 100644 --- a/config/nginx.background.conf +++ b/config/nginx.background.conf @@ -53,22 +53,38 @@ http { # the server will close connections after this time keepalive_timeout 600; - location /validator { - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - proxy_set_header Host $http_host; - proxy_set_header X-Forwarded-Proto $scheme; - proxy_set_header X-Forwarded-Port $server_port; - proxy_redirect off; - proxy_set_header Connection ''; - proxy_http_version 1.1; - chunked_transfer_encoding off; - proxy_buffering off; - proxy_cache off; +# location /validator { +# proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; +# proxy_set_header Host $http_host; +# proxy_set_header X-Forwarded-Proto $scheme; +# proxy_set_header X-Forwarded-Port $server_port; +# proxy_redirect off; +# proxy_set_header Connection ''; +# proxy_http_version 1.1; +# chunked_transfer_encoding off; +# proxy_buffering off; +# proxy_cache off; +# +# proxy_pass http://fhir_validator_app; +# } - proxy_pass http://fhir_validator_app; - } +# location /validatorapi/ { +# proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; +# proxy_set_header Host $http_host; +# proxy_set_header X-Forwarded-Proto $scheme; +# proxy_set_header X-Forwarded-Port $server_port; +# proxy_redirect off; +# proxy_set_header Connection ''; +# proxy_http_version 1.1; +# chunked_transfer_encoding off; +# proxy_buffering off; +# proxy_cache off; +# +# proxy_pass http://validator_service:4567/; +# } +# } - location /validatorapi/ { + location /hl7validatorapi/ { proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header Host $http_host; proxy_set_header X-Forwarded-Proto $scheme; @@ -79,8 +95,9 @@ http { chunked_transfer_encoding off; proxy_buffering off; proxy_cache off; + proxy_read_timeout 600s; - proxy_pass http://validator_service:4567/; + proxy_pass http://hl7_validator_service:3500/; } } } diff --git a/config/nginx.conf b/config/nginx.conf index af4b461..a49b549 100644 --- a/config/nginx.conf +++ b/config/nginx.conf @@ -68,7 +68,37 @@ http { proxy_pass http://inferno:4567; } - location /validator { +# location /validator { +# proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; +# proxy_set_header Host $http_host; +# proxy_set_header X-Forwarded-Proto $scheme; +# proxy_set_header X-Forwarded-Port $server_port; +# proxy_redirect off; +# proxy_set_header Connection ''; +# proxy_http_version 1.1; +# chunked_transfer_encoding off; +# proxy_buffering off; +# proxy_cache off; +# +# proxy_pass http://fhir_validator_app; +# } + +# location /validatorapi/ { +# proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; +# proxy_set_header Host $http_host; +# proxy_set_header X-Forwarded-Proto $scheme; +# proxy_set_header X-Forwarded-Port $server_port; +# proxy_redirect off; +# proxy_set_header Connection ''; +# proxy_http_version 1.1; +# chunked_transfer_encoding off; +# proxy_buffering off; +# proxy_cache off; +# +# proxy_pass http://validator_service:4567/; +# } + + location /hl7validatorapi/ { proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header Host $http_host; proxy_set_header X-Forwarded-Proto $scheme; @@ -79,23 +109,9 @@ http { chunked_transfer_encoding off; proxy_buffering off; proxy_cache off; + proxy_read_timeout 600s; - proxy_pass http://fhir_validator_app; - } - - location /validatorapi/ { - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - proxy_set_header Host $http_host; - proxy_set_header X-Forwarded-Proto $scheme; - proxy_set_header X-Forwarded-Port $server_port; - proxy_redirect off; - proxy_set_header Connection ''; - proxy_http_version 1.1; - chunked_transfer_encoding off; - proxy_buffering off; - proxy_cache off; - - proxy_pass http://validator_service:4567/; + proxy_pass http://hl7_validator_service:3500/; } } } diff --git a/docker-compose.background.yml b/docker-compose.background.yml index 134f14f..140aa91 100644 --- a/docker-compose.background.yml +++ b/docker-compose.background.yml @@ -1,17 +1,28 @@ version: '3' services: - validator_service: - image: infernocommunity/fhir-validator-service - # Update this path to match your directory structure + hl7_validator_service: + image: infernocommunity/inferno-resource-validator + environment: + # Defines how long validator sessions last if unused, in minutes: + # Negative values mean sessions never expire, 0 means sessions immediately expire + SESSION_CACHE_DURATION: -1 volumes: - ./lib/davinci_plan_net_test_kit/igs:/home/igs - fhir_validator_app: - image: infernocommunity/fhir-validator-app - depends_on: - - validator_service - environment: - EXTERNAL_VALIDATOR_URL: http://localhost/validatorapi - VALIDATOR_BASE_PATH: /validator + # To let the service share your local FHIR package cache, + # uncomment the below line + # - ~/.fhir:/home/ktor/.fhir + # validator_service: + # image: infernocommunity/fhir-validator-service + # # Update this path to match your directory structure + # volumes: + # - ./lib/davinci_plan_net_test_kit/igs:/home/igs + # fhir_validator_app: + # image: infernocommunity/fhir-validator-app + # depends_on: + # - validator_service + # environment: + # EXTERNAL_VALIDATOR_URL: http://localhost/validatorapi + # VALIDATOR_BASE_PATH: /validator nginx: image: nginx volumes: @@ -19,8 +30,8 @@ services: ports: - "80:80" command: [nginx, '-g', 'daemon off;'] - depends_on: - - fhir_validator_app + # depends_on: + # - fhir_validator_app redis: image: redis ports: diff --git a/docker-compose.yml b/docker-compose.yml index c937607..16ab428 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -6,7 +6,8 @@ services: volumes: - ./data:/opt/inferno/data depends_on: - - validator_service + - hl7_validator_service + # - validator_service worker: build: context: ./ @@ -15,14 +16,18 @@ services: command: bundle exec sidekiq -r ./worker.rb depends_on: - redis - validator_service: + hl7_validator_service: extends: file: docker-compose.background.yml - service: validator_service - fhir_validator_app: - extends: - file: docker-compose.background.yml - service: fhir_validator_app + service: hl7_validator_service + # validator_service: + # extends: + # file: docker-compose.background.yml + # service: validator_service + # fhir_validator_app: + # extends: + # file: docker-compose.background.yml + # service: fhir_validator_app nginx: extends: file: docker-compose.background.yml diff --git a/lib/davinci_plan_net_test_kit/generated/v1.1.0/davinci_plan_net_test_suite.rb b/lib/davinci_plan_net_test_kit/generated/v1.1.0/davinci_plan_net_test_suite.rb index c1ffd89..d227f13 100644 --- a/lib/davinci_plan_net_test_kit/generated/v1.1.0/davinci_plan_net_test_suite.rb +++ b/lib/davinci_plan_net_test_kit/generated/v1.1.0/davinci_plan_net_test_suite.rb @@ -141,6 +141,7 @@ class DaVinciPlanNetServerTestSuite < Inferno::TestSuite %r{Sub-extension url 'introspect' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris}, %r{Sub-extension url 'revoke' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris}, /Observation\.effective\.ofType\(Period\): .*us-core-1:/, # Invalid invariant in US Core v3.1.1 + /\A\S+: \S+: URL value '.*' does not resolve/, ].freeze VERSION_SPECIFIC_MESSAGE_FILTERS = [].freeze @@ -151,8 +152,11 @@ def self.metadata end end - validator do - url ENV.fetch('V110_VALIDATOR_URL', 'http://validator_service:4567') + id :davinci_plan_net_server_v110 + + fhir_resource_validator do + igs 'hl7.fhir.us.davinci-pdex-plan-net#1.1.0' + message_filters = VALIDATION_MESSAGE_FILTERS + VERSION_SPECIFIC_MESSAGE_FILTERS exclude_message do |message| @@ -180,8 +184,6 @@ def self.metadata } ] - id :davinci_plan_net_server_v110 - input :url, title: 'FHIR Endpoint', description: 'URL of the FHIR endpoint' diff --git a/lib/davinci_plan_net_test_kit/generator/suite_generator.rb b/lib/davinci_plan_net_test_kit/generator/suite_generator.rb index 602bf14..6676391 100644 --- a/lib/davinci_plan_net_test_kit/generator/suite_generator.rb +++ b/lib/davinci_plan_net_test_kit/generator/suite_generator.rb @@ -53,8 +53,9 @@ def title "DaVinci Plan Net #{ig_metadata.ig_version} Server Test Suite" end - def validator_env_name - "#{ig_metadata.reformatted_version.upcase}_VALIDATOR_URL" + def ig_identifier + version = ig_metadata.ig_version[1..] # Remove leading 'v' + "hl7.fhir.us.davinci-pdex-plan-net##{version}" end def ig_link diff --git a/lib/davinci_plan_net_test_kit/generator/templates/suite.rb.erb b/lib/davinci_plan_net_test_kit/generator/templates/suite.rb.erb index 828f0d0..0223934 100644 --- a/lib/davinci_plan_net_test_kit/generator/templates/suite.rb.erb +++ b/lib/davinci_plan_net_test_kit/generator/templates/suite.rb.erb @@ -133,6 +133,7 @@ module DaVinciPlanNetTestKit %r{Sub-extension url 'introspect' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris}, %r{Sub-extension url 'revoke' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris}, /Observation\.effective\.ofType\(Period\): .*us-core-1:/, # Invalid invariant in US Core v3.1.1 + /\A\S+: \S+: URL value '.*' does not resolve/, ].freeze VERSION_SPECIFIC_MESSAGE_FILTERS = <%=version_specific_message_filters%>.freeze @@ -143,8 +144,11 @@ module DaVinciPlanNetTestKit end end - validator do - url ENV.fetch('<%= validator_env_name %>', 'http://validator_service:4567') + id :<%= suite_id %> + + fhir_resource_validator do + igs '<%= ig_identifier %>' + message_filters = VALIDATION_MESSAGE_FILTERS + VERSION_SPECIFIC_MESSAGE_FILTERS exclude_message do |message| @@ -172,8 +176,6 @@ module DaVinciPlanNetTestKit } ] - id :<%= suite_id %> - input :url, title: 'FHIR Endpoint', description: 'URL of the FHIR endpoint' diff --git a/lib/davinci_plan_net_test_kit/igs/README.md b/lib/davinci_plan_net_test_kit/igs/README.md new file mode 100644 index 0000000..644c908 --- /dev/null +++ b/lib/davinci_plan_net_test_kit/igs/README.md @@ -0,0 +1,21 @@ +# Note on this IGs folder + +There are three reasons why it would be necessary to put an IG package.tgz in this folder. If none of these apply, you do not need to put any files here, or can consider removing any existing files to make it clear they are unused. + +## 1. Generated Test Suites +Some test kits use a "generator" to automatically generate the contents of a test suite for an IG. The IG files are required every time the test suites need to be regenerated. Examples of test kits that use this approach are the US Core Test Kit and CARIN IG for Blue Button® Test Kit. + + +## 2. Non-published IG +If your IG, or the specific version of the IG you want to test against, is not published, then the validator service needs to load the IG from file in order to be able to validate resources with it. The IG must be referenced in the `fhir_resource_validator` block in the test suite definition by filename, ie: + +```ruby + fhir_resource_validator do + igs 'igs/filename.tgz' + + ... + end +``` + +## 3. Inferno Validator UI +The Inferno Validator UI is configured to auto-load any IGs present in the igs folder and include them in all validations. The Inferno Validator UI is currently disabled by default, so this is only relevant if you choose to re-enable it. In general, the Inferno team is currently leaving IGs in this folder even if not otherwise necessary to make it easy to re-enable the validator UI. \ No newline at end of file diff --git a/lib/davinci_plan_net_test_kit/reference_resolution_test.rb b/lib/davinci_plan_net_test_kit/reference_resolution_test.rb index b98a849..e51ffa1 100644 --- a/lib/davinci_plan_net_test_kit/reference_resolution_test.rb +++ b/lib/davinci_plan_net_test_kit/reference_resolution_test.rb @@ -165,7 +165,8 @@ def resource_is_valid_with_target_profile?(resource, target_profile) target_profile_with_version = target_profile.include?('|') ? target_profile : "#{target_profile}|#{metadata.profile_version}" - outcome = FHIR::OperationOutcome.new(JSON.parse(validator.validate(resource, target_profile_with_version))) + validator_response = validator.validate(resource, target_profile_with_version) + outcome = validator.operation_outcome_from_hl7_wrapped_response(validator_response) message_hashes = outcome.issue&.map { |issue| validator.message_hash_from_issue(issue, resource) } || []