onc_certification_g10_test_kit 6.0.3 → 7.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 652df76ad9ffd8a3ab99ab73a34246cc282820dbb480847c2bfedd2109b3d523
-  data.tar.gz: 6a9c481e3daec6bcf67275e5f52412a09df62b76f6694bbf29578a9dd659274e
+  metadata.gz: a7c3b147bf3895a43988f8d02e947ac646522fb0637c6bb33ca7d00fe6d8728b
+  data.tar.gz: b7a1f24fb4775b196f1eb48ba8bb995754580dbbd48c1dd1e066e56cb3e8cc45
 SHA512:
-  metadata.gz: 0bf954379978636a9ae036e564102b5b4b741994778100937c847fdb54003ef7560ca102f98f47588fac71f533b5c90772a17517354406a7edae731a0be2e91e
-  data.tar.gz: be29443df38b70553a074af1ef53f03553d4da9cd51ffccd5dca3927a82b39d4829bcf60e53c4d70ca6f8c2ce200ff9498cc9f27aeb18bb58e48d3353fdd7eee
+  metadata.gz: 48b3460861a86ba5358b79351fd75d0335ba7cb75a575f7e92780bee257719c0947d79f1670481187b392376888f606384a6a84c38f441f6411cb14d3f726926
+  data.tar.gz: 16f84edff5ac43c598d0876f2d7ec4f78d8e7d661d08bcd679d243006b00329a258d78429485d74bf60bcfd5810ec703c36e5b6ee963b082b2787ec80a331511

data/lib/inferno/repositiories/validators.rb

@@ -3,12 +3,6 @@ require 'inferno/repositories/in_memory_repository'
 module Inferno
   module Repositories
     class Validators < InMemoryRepository
-      def self.index_by_id
-        @all_by_id = {}
-        all.each { |vs| @all_by_id[vs.url] = vs }
-        @all_by_id
-      end
-
       def all_urls
         all_by_id.keys
       end

data/lib/inferno/repositiories/value_sets.rb

@@ -3,15 +3,9 @@ require 'inferno/repositories/in_memory_repository'
 module Inferno
   module Repositories
     class ValueSets < InMemoryRepository
-      def self.index_by_id
-        @all_by_id = {}
-        all.each { |vs| @all_by_id[vs.url] = vs }
-        @all_by_id
-      end
-
       # @return [Hash] a Hash where the keys are vs urls and the values are vs
       def select_by_url(urls)
-        self.class.all_by_id.slice(*urls)
+        all_by_id.slice(*urls)
       end
 
       def select_by_binding_strength(strengths)

data/lib/inferno/terminology/expected_manifest.yml

@@ -121,7 +121,7 @@
   - http://hl7.org/fhir/composition-status
 - :url: http://hl7.org/fhir/us/core/ValueSet/us-core-documentreference-type
   :file: hl7_org_fhir_us_core_ValueSet_us-core-documentreference-type.msgpack
-  :count: 11418
+  :count: 12002
   :type: bloom
   :code_systems:
   - http://terminology.hl7.org/CodeSystem/v3-NullFlavor
@@ -134,7 +134,7 @@
   - http://hl7.org/fhir/document-relationship-type
 - :url: http://hl7.org/fhir/ValueSet/mimetypes
   :file: hl7_org_fhir_ValueSet_mimetypes.msgpack
-  :count: 2503
+  :count: 2578
   :type: bloom
   :code_systems:
   - urn:ietf:bcp:13
@@ -504,7 +504,7 @@
   :code_systems: http://terminology.hl7.org/CodeSystem/v3-NullFlavor
 - :url: http://loinc.org
   :file: loinc_org.msgpack
-  :count: 287148
+  :count: 292887
   :type: bloom
   :code_systems: http://loinc.org
 - :url: http://hl7.org/fhir/document-relationship-type
@@ -514,7 +514,7 @@
   :code_systems: http://hl7.org/fhir/document-relationship-type
 - :url: urn:ietf:bcp:13
   :file: urn_ietf_bcp_13.msgpack
-  :count: 2503
+  :count: 2578
   :type: bloom
   :code_systems: urn:ietf:bcp:13
 - :url: http://hl7.org/fhir/identifier-use
@@ -669,7 +669,7 @@
   :code_systems: http://terminology.hl7.org/CodeSystem/observation-category
 - :url: http://snomed.info/sct
   :file: snomed_info_sct.msgpack
-  :count: 508538
+  :count: 517626
   :type: bloom
   :code_systems: http://snomed.info/sct
 - :url: http://terminology.hl7.org/CodeSystem/data-absent-reason

data/lib/inferno/terminology/fhir_package_manager.rb

@@ -10,6 +10,8 @@ module Inferno
     module FHIRPackageManager
       class << self
         REGISTRY_SERVER_URL = 'https://packages.fhir.org'.freeze
+        US_CORE_7_PACKAGE_URL = 'https://hl7.org/fhir/us/core/STU7/package.tgz'.freeze
+        VSAC_18_PACKAGE_URL = 'https://packages2.fhir.org/packages/us.nlm.vsac/0.18.0'.freeze
         REQUIRED_VSAC_VALUE_SET_URLS = [
           'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.836',
           'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.1.11.14914',
@@ -44,10 +46,17 @@ module Inferno
         #
         # @param [String] package The FHIR Package
         def get_package(package, destination, desired_types = [])
-          package_url = package
-            .split('#')
-            .prepend(REGISTRY_SERVER_URL)
-            .join('/')
+          package_url = case package
+                        when 'hl7.fhir.us.core#7.0.0'
+                          US_CORE_7_PACKAGE_URL
+                        when 'us.nlm.vsac#0.18.0'
+                          VSAC_18_PACKAGE_URL
+                        else
+                          package
+                            .split('#')
+                            .prepend(REGISTRY_SERVER_URL)
+                            .join('/')
+                        end
 
           tar_file_name = "tmp/#{package.split('#').join('-')}.tgz"
 

data/lib/inferno/terminology/loader.rb

@@ -199,7 +199,8 @@ module Inferno
             USCoreTestKit::USCoreV311::USCoreTestSuite.metadata +
             USCoreTestKit::USCoreV400::USCoreTestSuite.metadata +
             USCoreTestKit::USCoreV501::USCoreTestSuite.metadata +
-            USCoreTestKit::USCoreV610::USCoreTestSuite.metadata
+            USCoreTestKit::USCoreV610::USCoreTestSuite.metadata +
+            USCoreTestKit::USCoreV700::USCoreTestSuite.metadata
 
           all_metadata =
             all_metadata

data/lib/inferno/terminology/tasks/download_fhir_terminology.rb

@@ -19,8 +19,9 @@ module Inferno
           FHIRPackageManager.get_package('hl7.fhir.us.core#4.0.0', PACKAGE_DIR, ['ValueSet', 'CodeSystem'])
           FHIRPackageManager.get_package('hl7.fhir.us.core#5.0.1', PACKAGE_DIR, ['ValueSet', 'CodeSystem'])
           FHIRPackageManager.get_package('hl7.fhir.us.core#6.1.0', PACKAGE_DIR, ['ValueSet', 'CodeSystem'])
+          FHIRPackageManager.get_package('hl7.fhir.us.core#7.0.0', PACKAGE_DIR, ['ValueSet', 'CodeSystem'])
           FHIRPackageManager.get_package(
-            'us.nlm.vsac#0.11.0', File.join(PACKAGE_DIR, 'vsac'), ['ValueSet', 'CodeSystem']
+            'us.nlm.vsac#0.18.0', File.join(PACKAGE_DIR, 'vsac'), ['ValueSet', 'CodeSystem']
           )
         end
 

data/lib/inferno/terminology/tasks/download_umls.rb

@@ -13,7 +13,8 @@ module Inferno
           '2020' => 'https://download.nlm.nih.gov/umls/kss/2020AB/umls-2020AB-full.zip',
           '2021' => 'https://download.nlm.nih.gov/umls/kss/2021AA/umls-2021AA-full.zip',
           '2022' => 'https://download.nlm.nih.gov/umls/kss/2022AA/umls-2022AA-full.zip',
-          '2023' => 'https://download.nlm.nih.gov/umls/kss/2023AA/umls-2023AA-full.zip'
+          '2023' => 'https://download.nlm.nih.gov/umls/kss/2023AA/umls-2023AA-full.zip',
+          '2024' => 'https://download.nlm.nih.gov/umls/kss/2024AA/umls-2024AA-full.zip'
         }.freeze
         TICKET_GRANTING_TICKET_URL = 'https://utslogin.nlm.nih.gov/cas/v1/api-key'.freeze
 

data/lib/inferno/terminology/tasks/expand_value_set_to_file.rb

@@ -16,7 +16,7 @@ module Inferno
           # Before writing the JSON to a file at the end
           end_vs = nil if type == 'json'
 
-          %w[2023].each do |version|
+          %w[2024].each do |version|
             Loader.register_umls_db File.join(TEMP_DIR, version, 'umls.db')
             Loader.load_value_sets_from_directory(PACKAGE_DIR, true)
             vs = Repositories::ValueSets.new.find(value_set_url)

data/lib/inferno/terminology/tasks/run_umls_jar.rb

@@ -13,7 +13,8 @@ module Inferno
           '2020' => 'inferno_2020.prop',
           '2021' => 'inferno_2021.prop',
           '2022' => 'inferno_2022.prop',
-          '2023' => 'inferno_2023.prop'
+          '2023' => 'inferno_2023.prop',
+          '2024' => 'inferno_2024.prop'
         }.freeze
 
         attr_reader :version

data/lib/inferno/terminology/validator.rb

@@ -4,6 +4,7 @@ module Inferno
   module Terminology
     class Validator
       attr_reader :url, :concept_count, :type, :code_systems, :file_name, :bloom_filter
+      alias id url
 
       def initialize(metadata)
         @url = metadata[:url]

data/lib/inferno/terminology/value_set.rb

@@ -193,6 +193,8 @@ module Inferno
         @value_set_model.url
       end
 
+      alias id url
+
       # Return the number of codes in the valueset
       def count
         @value_set.length

data/lib/onc_certification_g10_test_kit/all_resources.rb

@@ -0,0 +1,74 @@
+require_relative 'g10_options'
+
+module ONCCertificationG10TestKit
+  # This is a list of all resource types mapped to USCDI data classes or elements,
+  # and shall be supported by certified server implementation:
+
+  # * AllergyIntolerance
+  # * CarePlan
+  # * CareTeam
+  # * Condition
+  # * Device
+  # * DiagnosticReport
+  # * DocumentReference
+  # * Encounter
+  # * Goal
+  # * Immunization
+  # * MedicationRequest
+  # * Observation
+  # * Organization
+  # * Patient
+  # * Practitioner
+  # * Procedure
+  # * Provenance
+
+  # For USCDI v2 / US Core v5.0.1, these resource types are added:
+  # * RelatedPerson
+  # * ServiceRequest
+
+  # For USCDI v3 / US Core v6.1.0, these resource types are added:
+  # * Coverage
+  # * MedicationDispense
+  # * Specimen
+
+  # For USCDI v4 / US Core v7.0.0, these resource types are added:
+  # * Location
+  module AllResources
+    ALL_RESOURCES =
+      [
+        'AllergyIntolerance',
+        'CarePlan',
+        'CareTeam',
+        'Condition',
+        'Device',
+        'DiagnosticReport',
+        'DocumentReference',
+        'Encounter',
+        'Goal',
+        'Immunization',
+        'MedicationRequest',
+        'Observation',
+        'Organization',
+        'Procedure',
+        'Patient',
+        'Practitioner',
+        'Provenance'
+      ].freeze
+
+    V5_ALL_RESOURCES = (ALL_RESOURCES + ['RelatedPerson', 'ServiceRequest']).freeze
+
+    V6_ALL_RESOURCES = (V5_ALL_RESOURCES + ['Coverage', 'MedicationDispense', 'Specimen']).freeze
+
+    V7_ALL_RESOURCES = (V6_ALL_RESOURCES + ['Location']).freeze
+
+    def all_required_resources
+      return V5_ALL_RESOURCES if using_us_core_5?
+
+      return V6_ALL_RESOURCES if using_us_core_6?
+
+      return V7_ALL_RESOURCES if using_us_core_7?
+
+      ALL_RESOURCES
+    end
+  end
+end