FI-3100: Update (g)(10) Certfication Test Kit Terminology Package to …

…2024 Version (#570) * Update terminology script to pull down 2024 UMLS files * Fix vsac package version and check explicitly for full us core package name in fhir package manager * Update fhir package manager to use package2 url for updated vsac package * Update value sets yml file to include the VS bindings from US Core 7
onc-healthit · Oct 22, 2024 · fe9ab4a · fe9ab4a
1 parent f2c7a12
commit fe9ab4a
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Showing 13 changed files with 132 additions and 20 deletions.
diff --git a/Rakefile b/Rakefile
@@ -29,7 +29,7 @@ Inferno.logger.formatter = proc do |_severity, _datetime, _progname, message|
   "#{message}\n"
 end
 
-default_version = '2023'
+default_version = '2024'
 
 namespace :terminology do |_argv|
   desc 'download and execute UMLS terminology data'

diff --git a/bin/create_umls.sh b/bin/create_umls.sh
@@ -4,7 +4,7 @@ if [ -n "$1" ]
 then
   version="$1"
 else
-  version="2023"
+  version="2024"
 fi
 
 echo "Version: ${version}"

diff --git a/bin/prepare_terminology.sh b/bin/prepare_terminology.sh
@@ -5,7 +5,7 @@ if [ -n "$1" ]
 then
   version="$1"
 else
-  version="2023"
+  version="2024"
 fi
 
 temp_folder="tmp/terminology/${version}"

diff --git a/bin/run_terminology.sh b/bin/run_terminology.sh
@@ -11,12 +11,12 @@ if [ -f /.dockerenv ]; then
   fi
 fi
 
-./bin/prepare_terminology.sh 2023
+./bin/prepare_terminology.sh 2024
 bundle exec rake terminology:create_vs_validators["preferred"]
 echo "$?"
 
 if [ -n "$CLEANUP" ]
 then
-    echo 'Deleting 2023 build files'
-    bundle exec rake terminology:cleanup_precursors["2023"]
+    echo 'Deleting 2024 build files'
+    bundle exec rake terminology:cleanup_precursors["2024"]
 fi
diff --git a/lib/inferno/terminology/expected_manifest.yml b/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: 2575
   :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: 2575
   :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

diff --git a/lib/inferno/terminology/fhir_package_manager.rb b/lib/inferno/terminology/fhir_package_manager.rb
@@ -10,6 +10,8 @@ module Terminology
     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 @@ class << self
         #
         # @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"
 

diff --git a/lib/inferno/terminology/loader.rb b/lib/inferno/terminology/loader.rb
@@ -199,7 +199,8 @@ def save_new_value_set_list
             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

diff --git a/lib/inferno/terminology/tasks/download_fhir_terminology.rb b/lib/inferno/terminology/tasks/download_fhir_terminology.rb
@@ -19,8 +19,9 @@ def download_us_core
           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
 

diff --git a/lib/inferno/terminology/tasks/download_umls.rb b/lib/inferno/terminology/tasks/download_umls.rb
@@ -13,7 +13,8 @@ class DownloadUMLS
           '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
 

diff --git a/lib/inferno/terminology/tasks/expand_value_set_to_file.rb b/lib/inferno/terminology/tasks/expand_value_set_to_file.rb
@@ -16,7 +16,7 @@ def run
           # 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)

diff --git a/lib/inferno/terminology/tasks/run_umls_jar.rb b/lib/inferno/terminology/tasks/run_umls_jar.rb
@@ -13,7 +13,8 @@ class RunUMLSJar
           '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