Switch FHIR Server to CQF Ruler

dev/config/hapi/application.yaml

@@ -1,149 +1,104 @@
+# originally from:
+# https://raw.githubusercontent.com/DBCG/cqf-ruler/v0.7.1/server/src/main/resources/application.yaml
 spring:
-  jpa:
-    properties:
-      hibernate.format_sql: false
-      hibernate.show_sql: false
-#      hibernate.hbm2ddl.auto: update
-#      hibernate.jdbc.batch_size: 20
-#      hibernate.cache.use_query_cache: false
-#      hibernate.cache.use_second_level_cache: false
-#      hibernate.cache.use_structured_entries: false
-#      hibernate.cache.use_minimal_puts: false
-###    These settings will enable fulltext search with lucene
-      hibernate.search.enabled: true
-      hibernate.search.backend.type: lucene
-#      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer
-#      hibernate.search.backend.directory.type: local-filesystem
-#      hibernate.search.backend.directory.root: target/lucenefiles
-#      hibernate.search.backend.lucene_version: lucene_current
-  batch:
-    job:
-      enabled: false
-  main:
-#    TODO 5.6.0 -> Prevent duplicate bean definitions in the Spring batch config in HAPI: see:
-    allow-bean-definition-overriding: true
+   config:
+      import: classpath:org/opencds/cqf/external/application.yaml
+---
+spring:
+   main:
+      allow-bean-definition-overriding: true # the cqf-ruler plugins override serveral upstream hapi beans
+---
 hapi:
-  fhir:
-    ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5
-    fhir_version: R4
-### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers
-### to determine the FHIR server address
-#   use_apache_address_strategy: false
-### forces the use of the https:// protocol for the returned server address.
-### alternatively, it may be set using the X-Forwarded-Proto header.
-#   use_apache_address_strategy_https: false
-### enable to set the Server URL
-#    server_address: http://hapi.fhir.org/baseR4
-#    defer_indexing_for_codesystems_of_size: 101
-#    install_transitive_ig_dependencies: true
-#    implementationguides:
-###    example from registry (packages.fhir.org)
-#      swiss:
-#        name: swiss.mednet.fhir
-#        version: 0.8.0
-#      example not from registry
-#      ips_1_0_0:
-#        url: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
-#        name: hl7.fhir.uv.ips
-#        version: 1.0.0
-#    supported_resource_types:
-#      - Patient
-#      - Observation
-#    allow_cascading_deletes: true
-#    allow_contains_searches: true
-#    allow_external_references: true
-#    allow_multiple_delete: true
-#    allow_override_default_search_params: true
-#    auto_create_placeholder_reference_targets: false
-#    cql_enabled: true
-#    default_encoding: JSON
-#    default_pretty_print: true
-#    default_page_size: 20
-#    delete_expunge_enabled: true
-#    enable_repository_validating_interceptor: false
-#    enable_index_missing_fields: false
-#    enable_index_contained_resource: false
-#    enforce_referential_integrity_on_delete: false
-#    enforce_referential_integrity_on_write: false
-#    etag_support_enabled: true
-#    expunge_enabled: true
-#    daoconfig_client_id_strategy: null
-#    client_id_strategy: ALPHANUMERIC
-#    fhirpath_interceptor_enabled: false
-#    filter_search_enabled: true
-#    graphql_enabled: true
-#    narrative_enabled: true
-#    mdm_enabled: true
-#    partitioning:
-#      allow_references_across_partitions: false
-#      partitioning_include_in_search_hashes: false
-    cors:
-      allow_Credentials: true
-      # These are allowed_origin patterns, see: https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/cors/CorsConfiguration.html#setAllowedOriginPatterns-java.util.List-
-      allowed_origin:
-        - '*'
+   fhir:
+      fhir_version: R4
+      allow_external_references: true
+      enforce_referential_integrity_on_delete: false
+      enforce_referential_integrity_on_write: false
+      cors:
+         allow_Credentials: true
+         allowed_origin:
+            - "*"
+      openapi_enabled: true
+      tester_enabled: true
+      tester:
+         home:
+            name: Local Tester
+            server_address: "http://localhost:8080/fhir"
+            refuse_to_fetch_third_party_urls: false
+            fhir_version: R4
+
+      ## CQL Settings
+      cql:
+         # enabled: true
+         engine:
+            # debug_logging_enabled: false
+            options: "EnableExpressionCaching"
+         # use_embedded_libraries: true
+         # translator:
+         #    analyzeDataRequirements: false
+         #    collapseDataRequirements: true
+         # options: "EnableAnnotations,EnableLocators,DisableListDemotion,DisableListPromotion"
+
+      ## RA Settings
+      ra:
+         #e enabled: true
+         report:
+            endpoint: ""
+
+      sdc:
+         # enabled: true
+         extract:
+            endpoint: "http://localhost:8080/fhir/"
+            username:
+            password:
+         transform:
+            enabled: true
+            replace_code:
+            username:
+            password:
+            endpoint:
+
+      ## Dev Tools Settings
+      devtools:
+         # enabled: true
+
+      ## Security settings
+      security:
+         # enabled: true
+         basic_auth:
+            enabled: false
+            username: someuser
+            password: thepassword
+         oauth:
+            enabled: false
+            securityCors: true
+            securityUrl: http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris
+            securityExtAuthUrl: authorize
+            securityExtAuthValueUri: http://launch.smarthealthit.org/v/r4/auth/authorize
+            securityExtTokenUrl: token
+            securityExtTokenValueUri: http://launch.smarthealthit.org/v/r4/auth/token
+            serviceSystem: http://hl7.org/fhir/restful-security-service
+            serviceCode: SMART-on-FHIR
+            serviceDisplay: SMART-on-FHIR
+            serviceText: OAuth2 using SMART-on-FHIR profile (see http://docs.smarthealthit.org)
 
-    # Search coordinator thread pool sizes
-    search-coord-core-pool-size: 20
-    search-coord-max-pool-size: 100
-    search-coord-queue-capacity: 200
+      ## CR Settings
+      cr:
+         enabled: true
+         measure_report:
+            care_gaps_reporter: Organization/alphora
+            care_gaps_composition_section_author: Organization/alphora-author
+         # measure_evaluation:
+         #    threaded_enabled: true
+         #    threaded_batch_size: 1000
+         #    num_threads: 8
 
-#    logger:
-#      error_format: 'ERROR - ${requestVerb} ${requestUrl}'
-#      format: >-
-#        Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
-#        Operation[${operationType} ${operationName} ${idOrResourceName}]
-#        UA[${requestHeader.user-agent}] Params[${requestParameters}]
-#        ResponseEncoding[${responseEncodingNoDefault}]
-#      log_exceptions: true
-#      name: fhirtest.access
-#    max_binary_size: 104857600
-#    max_page_size: 200
-#    retain_cached_searches_mins: 60
-#    reuse_cached_search_results_millis: 60000
-    tester:
-        home:
-          name: Local Tester
-          server_address: 'http://localhost:8080/fhir'
-          refuse_to_fetch_third_party_urls: false
-          fhir_version: R4
-        global:
-          name: Global Tester
-          server_address: "http://hapi.fhir.org/baseR4"
-          refuse_to_fetch_third_party_urls: false
-          fhir_version: R4
-#    validation:
-#      requests_enabled: true
-#      responses_enabled: true
-#    binary_storage_enabled: true
-#    bulk_export_enabled: true
-#    subscription:
-#      resthook_enabled: true
-#      websocket_enabled: false
-#      email:
-#        from: some@test.com
-#        host: google.com
-#        port:
-#        username:
-#        password:
-#        auth:
-#        startTlsEnable:
-#        startTlsRequired:
-#        quitWait:
-#    lastn_enabled: true
-###  This is configuration for normalized quantity serach level default is 0
-###   0: NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED - default
-###   1: NORMALIZED_QUANTITY_STORAGE_SUPPORTED
-###   2: NORMALIZED_QUANTITY_SEARCH_SUPPORTED
-#    normalized_quantity_search_level: 2
-#elasticsearch:
-#  debug:
-#    pretty_print_json_log: false
-#    refresh_after_write: false
-#  enabled: false
-#  password: SomePassword
-#  required_index_status: YELLOW
-#  rest_url: 'localhost:9200'
-#  protocol: 'http'
-#  schema_management_strategy: CREATE
-#  username: SomeUsername
+      ## CDS Hook Settings
+      cdshooks:
+         enabled: true
+         fhirserver:
+            expandValueSets: true
+            maxCodesPerQuery: 64
+            searchStyle: GET
+         prefetch:
+            maxUriLength: 8000

dev/docker-compose.yaml

@@ -53,18 +53,19 @@ services:
 
 
   fhir:
-    image: hapiproject/hapi:${FHIR_IMAGE_TAG:-v5.5.1}
+    image: ${FHIR_IMAGE_NAME:-alphora/cqf-ruler}:${FHIR_IMAGE_TAG:-0.8.1}
     environment:
       SPRING_CONFIG_LOCATION: file:///opt/application.yaml
       spring.datasource.url: jdbc:postgresql://db:5432/hapifhir
       spring.datasource.username: postgres
       spring.datasource.password: postgres
       spring.datasource.driverClassName: org.postgresql.Driver
-      spring.jpa.hibernate.dialect: org.hibernate.dialect.PostgreSQL94Dialect
+      spring.jpa.properties.hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
 
       # make URLs relative to fEMR for pagination
       # TODO remove when fEMR can rewrite URLs
       hapi.fhir.server_address: 'https://femr.${BASE_DOMAIN:-localtest.me}/fhir/'
+      hapi.fhir.tester.home.server_address: 'https://fhir.${BASE_DOMAIN:-localtest.me}/fhir/'
     volumes:
       - "./config/hapi/application.yaml:/opt/application.yaml:ro"
     depends_on: