From fe9ab4a628e3990ee03ce5998f3b7d90692ef0c5 Mon Sep 17 00:00:00 2001 From: Emily Semple <59289146+emichaud998@users.noreply.github.com> Date: Tue, 22 Oct 2024 14:09:54 -0400 Subject: [PATCH] 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 --- Rakefile | 2 +- bin/create_umls.sh | 2 +- bin/prepare_terminology.sh | 2 +- bin/run_terminology.sh | 6 +- lib/inferno/terminology/expected_manifest.yml | 10 +-- .../terminology/fhir_package_manager.rb | 17 +++-- lib/inferno/terminology/loader.rb | 3 +- .../tasks/download_fhir_terminology.rb | 3 +- .../terminology/tasks/download_umls.rb | 3 +- .../tasks/expand_value_set_to_file.rb | 2 +- lib/inferno/terminology/tasks/run_umls_jar.rb | 3 +- resources/inferno_2024.prop | 34 ++++++++++ resources/value_sets.yml | 65 +++++++++++++++++++ 13 files changed, 132 insertions(+), 20 deletions(-) create mode 100644 resources/inferno_2024.prop diff --git a/Rakefile b/Rakefile index d82a9715..8f24af97 100644 --- 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 index 0e914635..b6cc455e 100755 --- 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 index e665f833..97336782 100755 --- 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 index 092ef045..775251cd 100755 --- 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 index e088f080..ab3455a9 100644 --- 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 index 1ebf4b00..164f3d7d 100644 --- 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 index 9e1693a4..96ffe566 100644 --- 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 index acc87ecb..3d22beb1 100644 --- 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 index 7e4d57d7..9e92745b 100644 --- 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 index f7c059a7..d71e089d 100644 --- 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 index b1839c5b..8187260f 100644 --- 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 diff --git a/resources/inferno_2024.prop b/resources/inferno_2024.prop new file mode 100644 index 00000000..57d37145 --- /dev/null +++ b/resources/inferno_2024.prop @@ -0,0 +1,34 @@ +# Configuration Properties File +# Thu Nov 19 08:56:24 EST 2020 +mmsys_output_stream=gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream +gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.remove_obsolete_data=false +gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.confirm_selections=true +install_lvg=false +gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.calculate_md5s=false +release_version=2024AA +gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.suppressed_sabttys=ALT|AB;CCPSS|TC;CDT|OP;CPT|AB;FMA|AB;FMA|IS;FMA|OP;GO|IS;GO|MTH_IS;GO|MTH_OET;GO|MTH_OP;GO|OET;GO|OP;HCDT|AB;HCDT|OA;HCDT|OP;HCPCS|AB;HCPCS|AM;HCPCS|OA;HCPCS|OAM;HCPCS|OM;HCPCS|OP;HCPT|AB;HCPT|AM;HCPT|OA;HCPT|OP;HL7V3.0|ONP;HL7V3.0|OP;HPO|IS;HPO|OP;ICD10|HS;ICD10|PS;ICD10AE|HS;ICD10AE|PS;ICD10AM|PS;ICD10AMAE|PS;ICD10CM|AB;ICD10PCS|AB;ICD10PCS|HS;ICD9CM|AB;ICPC|CS;ICPC|PS;ICPC2EENG|AB;ICPC2P|MTH_OP;ICPC2P|MTH_OPN;ICPC2P|MTH_PT;ICPC2P|OP;ICPC2P|OPN;LNC|LO;LNC|MTH_LO;LNC|OLC;LNC|OOSN;LNC-DE-AT|LO;LNC-DE-CH|OOSN;LNC-DE-DE|LO;LNC-EL-GR|LO;LNC-ES-AR|LO;LNC-ES-AR|OOSN;LNC-ES-CH|OOSN;LNC-ES-ES|LO;LNC-ET-EE|LO;LNC-FR-BE|LO;LNC-FR-CA|LO;LNC-FR-CH|OOSN;LNC-FR-FR|LO;LNC-FR-FR|OLC;LNC-IT-CH|OOSN;LNC-IT-IT|LO;LNC-KO-KR|LO;LNC-NL-NL|LO;LNC-PT-BR|LO;LNC-PT-BR|OOSN;LNC-RU-RU|LO;LNC-TR-TR|LO;LNC-ZH-CN|LO;MDR|AB;MDR|MTH_OL;MDR|OL;MDRCZE|AB;MDRCZE|OL;MDRDUT|AB;MDRDUT|OL;MDRFRE|AB;MDRFRE|OL;MDRGER|AB;MDRGER|OL;MDRHUN|AB;MDRHUN|OL;MDRITA|AB;MDRITA|OL;MDRJPN|OL;MDRJPN|OLJKN;MDRJPN|OLJKN1;MDRPOR|AB;MDRPOR|OL;MDRRUS|AB;MDRRUS|OL;MDRSPA|AB;MDRSPA|OL;MSH|DEV;MSH|DSV;MSH|QAB;MSH|QEV;MSH|QSV;MSHGER|DSV;MSHNOR|DSV;MTHICPC2EAE|AB;NCBI|AUN;NCBI|UAUN;NCI|OP;NCI_NICHD|OP;NEU|ACR;NEU|IS;NEU|OP;NUCCHCPT|MP;PDQ|IS;PDQ|OP;RCD|AA;RCD|AB;RCD|AS;RCD|IS;RCD|OA;RCD|OP;RCDAE|AA;RCDAE|AB;RCDAE|IS;RCDAE|OA;RCDAE|OP;RCDSA|AB;RCDSA|IS;RCDSA|OA;RCDSA|OP;RCDSY|AB;RCDSY|IS;RCDSY|OA;RCDSY|OP;SCTSPA|IS;SCTSPA|MTH_IS;SCTSPA|MTH_OAF;SCTSPA|MTH_OAP;SCTSPA|MTH_OAS;SCTSPA|MTH_OF;SCTSPA|MTH_OP;SCTSPA|OAF;SCTSPA|OAP;SCTSPA|OAS;SCTSPA|OF;SCTSPA|OP;SNMI|HX;SNMI|PX;SNMI|SX;SNOMEDCT_US|IS;SNOMEDCT_US|MTH_IS;SNOMEDCT_US|MTH_OAF;SNOMEDCT_US|MTH_OAP;SNOMEDCT_US|MTH_OAS;SNOMEDCT_US|MTH_OF;SNOMEDCT_US|MTH_OP;SNOMEDCT_US|OAF;SNOMEDCT_US|OAP;SNOMEDCT_US|OAS;SNOMEDCT_US|OF;SNOMEDCT_US|OP;SNOMEDCT_VET|IS;SNOMEDCT_VET|OAF;SNOMEDCT_VET|OAP;SNOMEDCT_VET|OAS;SNOMEDCT_VET|OF;SNOMEDCT_VET|OP 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+gov.nih.nlm.umls.mmsys.filter.SourceListFilter.enforce_dep_source_selection=true diff --git a/resources/value_sets.yml b/resources/value_sets.yml index e6959953..a8508973 100644 --- a/resources/value_sets.yml +++ b/resources/value_sets.yml @@ -777,3 +777,68 @@ :system: http://hl7.org/fhir/ValueSet/specimen-status :path: status :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-specimen +- :type: CodeableConcept + :strength: extensible + :system: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1240.8 + :path: value + :extensions: + - http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication-adherence + - medicationAdherence + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest +- :type: CodeableConcept + :strength: example + :system: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1267.11 + :path: value + :extensions: + - http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication-adherence + - informationSource + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest +- :type: code + :strength: required + :system: http://hl7.org/fhir/ValueSet/observation-status + :path: status + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-treatment-intervention-preference +- :type: code + :strength: required + :system: http://hl7.org/fhir/ValueSet/observation-status + :path: status + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-care-experience-preference +- :type: code + :strength: required + :system: http://hl7.org/fhir/ValueSet/observation-status + :path: status + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-average-blood-pressure +- :type: code + :strength: required + :system: http://hl7.org/fhir/ValueSet/quantity-comparator + :path: component.value.comparator + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-average-blood-pressure +- :type: CodeableConcept + :strength: extensible + :system: http://terminology.hl7.org/ValueSet/v3-TribalEntityUS + :path: value + :extensions: + - http://hl7.org/fhir/us/core/StructureDefinition/us-core-tribal-affiliation + - tribalAffiliation + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient +- :type: code + :strength: required + :system: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1021.24 + :path: value + :extensions: + - http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient +- :type: code + :strength: extensible + :system: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1240.3 + :path: value + :extensions: + - http://hl7.org/fhir/us/core/StructureDefinition/us-core-sex + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient +- :type: CodeableConcept + :strength: extensible + :system: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1021.32 + :path: value + :extensions: + - http://hl7.org/fhir/us/core/StructureDefinition/us-core-genderIdentity + :profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient \ No newline at end of file