hapi.application.yaml

# -------------------------------------------------------------------------------------
# Server & Spring Boot
# -------------------------------------------------------------------------------------
server:
  # Uncomment to serve FHIR under a non-default context path (e.g., /example/path/fhir)
  # servlet:
  #   context-path: /example/path
  port: 8080
  tomcat:
    # allow | as a separator in URLs
    relaxed-query-chars: "|"

management:
  # Actuator endpoints: only /actuator/health exposed by default
  endpoints:
    enabled-by-default: false
    web:
      exposure:
        include: "health"  # or "info,health,prometheus,metrics" or "*" for all
  endpoint:
    info:
      enabled: true
    metrics:
      enabled: true
    health:
      enabled: true
      probes:
        enabled: true
      group:
        liveness:
          include: [ "livenessState", "readinessState" ]
    prometheus:
      enabled: true
  prometheus:
    metrics:
      export:
        enabled: true

spring:
#  elasticsearch:
#    uris: http://localhost:9200
#    username: elastic
#    password: elastic
  # -------------------------------------------------------------------------------
  # Application Name
  # -------------------------------------------------------------------------------
  application:
    name: "@project.artifactId@"

  # -------------------------------------------------------------------------------
  # A. Spring AI — Model Context Protocol (MCP)
  # -------------------------------------------------------------------------------
  ai:
    # Run e.g. `npx @modelcontextprotocol/inspector` and connect to http://localhost:8080/mcp/messages using Streamable HTTP

    # Add the following to the MCP server settings file in e.g. cursor or claude (Desktop applications) for local debugging:
    #    cursor:
    #    {
    #      "mcpServers": {
    #        "hapi": {
    #          "url": "http://localhost:8080/mcp/messages"
    #        }
    #      }
    #    }
    #    or claude:
    #    {
    #      "mcpServers": {
    #        "hapi": {
    #          "command": "npx",
    #          "args": [
    #            "mcp-remote@latest",
    #            "http://localhost:8080/mcp/messages"
    #          ]
    #        }
    #      }
    #    }

    mcp:
      server:
        name: FHIR MCP Server
        version: 1.0.0
        instructions: "This server provides access to a FHIR RESTful API. You can use it to query FHIR resources, perform operations, and retrieve data in a structured format."
        enabled: true
        streamable-http:
          mcp-endpoint: /mcp/messages


  # -------------------------------------------------------------------------------
  # B. Core Spring
  # -------------------------------------------------------------------------------
  main:
    allow-bean-definition-overriding: false
    allow-circular-references: true
    banner-mode: off

  autoconfigure:
    # This exclude is only needed for setups not using Elasticsearch where the elasticsearch sniff is not needed.
    exclude: org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration

  flyway:
    enabled: false
    baseline-on-migrate: true
    fail-on-missing-locations: false

  datasource:
    # url: "jdbc:h2:file:./target/database/h2"
    url: jdbc:h2:mem:test_mem
    username: sa
    password: null
    driver-class-name: org.h2.Driver
    # max-active: 15     # (ignored with HikariCP; use hikari.maximum-pool-size)
    hikari:
      maximum-pool-size: 10

  jpa:
    properties:
      hibernate:
        format_sql: false
        show_sql: false
        # Hibernate dialect is auto-detected except for H2/Postgres.
        # If using H2:     ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
        # If using Postgres: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
        dialect: ${HIBERNATE_DIALECT:ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect}

        # --- Optional Hibernate DDL & tuning (commented out from source) ---
        hbm2ddl:
          auto: update
        jdbc:
          batch_size: 20
        cache:
          use_query_cache: false
          use_second_level_cache: false
          use_structured_entries: false
          use_minimal_puts: false

        # --- Hibernate Search (Lucene/Elasticsearch) ---
        #search:
        #  schema_management:
        #    strategy: CREATE
        #  enabled: true
          # Lucene backend (default example)
          # backend:
          #   type: lucene
          #   analysis:
          #     configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiLuceneAnalysisConfigurer
          #   directory:
          #     type: local-filesystem
          #     root: target/lucenefiles
          #   lucene_version: lucene_current
          # Elasticsearch backend (alternative) — see also hapi.fhir.elasticsearch section in docs
#          backend:
#            layout:
#              strategy: ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy
#            type: elasticsearch
#            protocol: http
#            analysis:
#              configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticsearchAnalysisConfigurer
#            scroll_timeout: 60
#            schema_management:
#              settings_file: ca/uhn/fhir/jpa/elastic/index-settings.json
#              minimal_required_status_wait_timeout: 10000
#              minimal_required_status: YELLOW
#
#            dynamic_mapping: true
#          indexing:
#            plan:
#              synchronization:
#                strategy: async


# -------------------------------------------------------------------------------------
# HAPI FHIR — grouped by domain
# -------------------------------------------------------------------------------------
hapi:
  fhir:

    # -------------------------------------------------------------------------------
    # A. Core Server & API
    # -------------------------------------------------------------------------------
    openapi_enabled: true                       # Swagger UI at /fhir/swagger-ui/index.html; API docs at /fhir/api-docs
    fhir_version: R4                            # DSTU2 | DSTU3 | R4 | R5
    # use_apache_address_strategy: false
    # use_apache_address_strategy_https: false
    # custom_content_path: ./custom               # folder name must be 'custom'
    # app_content_path: ./configs/app            # served under /web/app
    # server_address: http://hapi.fhir.org/baseR4
    # defer_indexing_for_codesystems_of_size: 101

    # -------------------------------------------------------------------------------
    # B. Implementation Guides (IG) & Package Install
    # -------------------------------------------------------------------------------
    ig_runtime_upload_enabled: true
    # validate_resource_status_for_package_upload: false   # default true
    # install_transitive_ig_dependencies: true
    # implementationguides:
    #   swiss:
    #     name: swiss.mednet.fhir
    #     version: 0.8.0
    #     reloadExisting: false
    #     installMode: STORE_AND_INSTALL
    #   ips_1_0_0:
    #     packageUrl: https://costateixeira.github.io/smart-ips-pilgrimage-fulltest/package.tgz
    #     name: smart.who.int.ips-pilgrimage-test
    #     version: 0.1.0
    #     installMode: STORE_AND_INSTALL
    # additionalResourceFolders:
    #   - example
    #   - example2
    # supported_resource_types:
    #   - Patient
    #   - Observation
    # allowed_bundle_types: COLLECTION,DOCUMENT,MESSAGE,TRANSACTION,TRANSACTIONRESPONSE,BATCH,BATCHRESPONSE,HISTORY,SEARCHSET

    # -------------------------------------------------------------------------------
    # C. Clinical Reasoning / CQL / Care Gaps / CDS Hooks
    # -------------------------------------------------------------------------------
    cr:
      enabled: false                            # exposes Clinical Reasoning operation endpoints
      caregaps:
        reporter: "default"
        section_author: "default"
      terminologyServerClientSettings:
        maxRetryCount: 3
        retryIntervalMillis: 1000
        timeoutSeconds: 30
        socketTimeout: 60
      cql:
        use_embedded_libraries: true
        # namespaces:                             # namespaces to be registered with the CQL engine
          # example
          # hl7.fhir.uv.cql: http://hl7.org/fhir/uv/cql
        compiler:
          # low-level compiler options (typically not needed)
          # validate_units: true
          # verify_only: false
          # compatibility_level: "1.5"
          error_level: Info
          signature_level: All
          # analyze_data_requirements: false
          # collapse_data_requirements: false
          # translator_format: JSON
          # enable_date_range_optimization: true
          enable_annotations: true
          enable_locators: true
          enable_results_type: true
          enable_detailed_errors: true
          # disable_list_traversal: false
          # disable_list_demotion: false
          # enable_interval_demotion: false
          # enable_interval_promotion: false
          # disable_method_invocation: false
          # require_from_keyword: false
          # disable_default_model_info_load: false
        runtime:
          debug_logging_enabled: false
          # enable_validation: false
          # enable_expression_caching: true
        terminology:
          valueset_preexpansion_mode: IGNORE         # USE_IF_PRESENT | REQUIRE | IGNORE
          valueset_expansion_mode: USE_EXPAND_OPERATION   # AUTO | USE_EXPANSION_OPERATION | PERFORM_NAIVE_EXPANSION
          valueset_membership_mode: USE_VALIDATE_CODE_OPERATION            # AUTO | USE_VALIDATE_CODE_OPERATION | USE_EXPANSION
          code_lookup_mode: USE_VALIDATE_CODE_OPERATION      # AUTO | USE_VALIDATE_CODE_OPERATION | USE_CODESYSTEM_URL
          remote_terminology:
            - url: '${ONTO_SERVER_URL}'
              client_interceptor_beans:
                - terminologyInterceptor
        data:
          search_parameter_mode: USE_SEARCH_PARAMETERS       # AUTO | USE_SEARCH_PARAMETERS | FILTER_IN_MEMORY
          terminology_parameter_mode: USE_VALUE_SET_URL       # AUTO | USE_VALUE_SET_URL | USE_INLINE_CODES | FILTER_IN_MEMORY
          profile_mode: DECLARED                             # ENFORCED | DECLARED | OPTIONAL | TRUST | OFF
    cdshooks:
      enabled: false
      clientIdHeaderName: client_id

    # -------------------------------------------------------------------------------
    # D. Search & Indexing
    # -------------------------------------------------------------------------------
    # NOTE: Extended Lucene/Elasticsearch indexing is experimental.
    # See https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
    # advanced_lucene_indexing: true
    # search_index_full_text_enabled: true
    # language_search_parameter_enabled: true
    # upliftedRefchains_enabled: true
    # index_storage_optimized: false
    # enable_index_missing_fields: false
    # enable_index_of_type: true
    # enable_index_contained_resource: false
    # store_resource_in_lucene_index_enabled: true

    # -------------------------------------------------------------------------------
    # Elasticsearch Configuration
    # -------------------------------------------------------------------------------
    # elasticsearch:
    #   index_prefix: "myprefix"   # Prefix for all Elasticsearch indexes (e.g., myprefix_observation_index)

    # -------------------------------------------------------------------------------
    # E. Bulk Operations
    # -------------------------------------------------------------------------------
    bulk_export_enabled: false
    bulk_import_enabled: false
    bulk_export_file_retention_period_hours: 2

    # -------------------------------------------------------------------------------
    # F. Write / Delete / Integrity
    # -------------------------------------------------------------------------------
    # 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
    # mass_ingestion_mode_enabled: false
    # auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
    # client_id_strategy: ALPHANUMERIC
    # server_id_strategy: SEQUENTIAL_NUMERIC
    # enforce_referential_integrity_on_delete: false
    # enforce_referential_integrity_on_write: false
    # etag_support_enabled: true
    # expunge_enabled: true
    # fhirpath_interceptor_enabled: false
    # filter_search_enabled: true
    # graphql_enabled: true

    # Thread pool configuration for maintenance operations
    # Defaults to Runtime.getRuntime().availableProcessors() if not specified
    # reindex_thread_count: 4        # Number of threads to use for reindex operations
    # expunge_thread_count: 4        # Number of threads to use for expunge operations
    # mark_resources_for_reindexing_upon_search_parameter_change: false

    # -------------------------------------------------------------------------------
    # G. Narrative & Validation
    # -------------------------------------------------------------------------------
    narrative_enabled: false
    # validation:
    #   requests_enabled: true
    #   responses_enabled: true

    # -------------------------------------------------------------------------------
    # H. MDM (Master Data Management)
    # -------------------------------------------------------------------------------
    mdm_enabled: false
    mdm_rules_json_location: "mdm-rules.json"
    # userRequestRetryVersionConflictsInterceptorEnabled: false

    # -------------------------------------------------------------------------------
    # I. Terminology / ValueSet Expansion
    # -------------------------------------------------------------------------------
    # pre_expand_value_sets: true
    # enable_task_pre_expand_value_sets: true
    # pre_expand_value_sets_default_count: 1000
    # pre_expand_value_sets_max_count: 1000
    # maximum_expansion_size: 1000
    logical_urls:
      - http://terminology.hl7.org/*
      - https://terminology.hl7.org/*
      - http://snomed.info/*
      - https://snomed.info/*
      #- http://unitsofmeasure.org/*
      #- https://unitsofmeasure.org/*
      #- http://loinc.org/*
      #- https://loinc.org/*
      # additional logical urls as per https://digital.nhs.uk/services/terminology-server
      - https://dmd.nhs.uk*              
      - http://hl7.org/fhir/sid/icd-10* 
      - https://icd.who.int/browse10*    
      - http://read.info*                
      - https://nicip.nhs.uk*            
      - http://www.datadictionary.nhs.uk/data_dictionary/attributes/o/opcs_4* 

    # -------------------------------------------------------------------------------
    # J. Partitioning & Multitenancy
    # -------------------------------------------------------------------------------
    # partitioning:
    #   allow_references_across_partitions: false
    #   partitioning_include_in_search_hashes: false
    #   default_partition_id: 0
    # database_partition_mode_enabled: true
    # patient_id_partitioning_mode: true
    # request_tenant_partitioning_mode: false

    # -------------------------------------------------------------------------------
    # K. CORS
    # -------------------------------------------------------------------------------
    cors:
      # allow_Credentials: false
      allowed_origin:
        - "*"
      # If you enable allow_Credentials=true, use explicit origins instead of "*".
      # Optional overrides. If omitted, built-in defaults are used.
      # allowed_headers:
      #   - Origin
      #   - Accept
      #   - Content-Type
      #   - Authorization
      #   - Cache-Control
      #   - If-Match
      #   - If-None-Match
      # exposed_headers:
      #   - Location
      #   - Content-Location
      #   - ETag
      # allowed_methods:
      #   - GET
      #   - POST
      #   - PUT
      #   - DELETE
      #   - OPTIONS
      #   - PATCH
      #   - HEAD

    # -------------------------------------------------------------------------------
    # L. Search Orchestration
    # -------------------------------------------------------------------------------
    search-coord-core-pool-size: 20
    search-coord-max-pool-size: 100
    search-coord-queue-capacity: 200
    # Search Prefetch Thresholds.
    # This setting sets the number of search results to prefetch. For example, if this list
    # is set to [100, 1000, -1] then the server will initially load 100 results and not
    # attempt to load more. If the user requests subsequent page(s) of results and goes
    # past 100 results, the system will load the next 900 (up to the following threshold of 1000).
    # The system will progressively work through these thresholds.
    # A threshold of -1 means to load all results. Note that if the final threshold is a
    # number other than -1, the system will never prefetch more than the given number.
    # CSV list; -1 as final value means "all"
    search_prefetch_thresholds: 13,503,2003,-1

    # -------------------------------------------------------------------------------
    # M. Extensibility (custom beans / interceptors / providers)
    # -------------------------------------------------------------------------------
    # comma-separated package names, will be @ComponentScan'ed by Spring to allow for creating custom Spring beans

    custom-bean-packages:
      - com.nhs
    # custom-interceptor-classes:
    # custom-provider-classes:
    
    # store_meta_source_information: NONE
    # bundle_batch_pool_size: 10
    # bundle_batch_pool_max_size: 50

    # -------------------------------------------------------------------------------
    # N. Logging
    # -------------------------------------------------------------------------------
    # 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

    # -------------------------------------------------------------------------------
    # O. Storage / Pagination / Caching
    # -------------------------------------------------------------------------------
    # max_binary_size: 104857600
    # max_page_size: 200
    # retain_cached_searches_mins: 60
    # reuse_cached_search_results_millis: 60000
    # binary_storage_enabled: true
    # binary_storage_mode: FILESYSTEM
    # binary_storage_filesystem_base_directory: /binstore
    # When binary_storage_mode is FILESYSTEM and this value is not set,
    # the starter defaults to 102400 bytes so smaller binaries stay inline.
    binary_storage_minimum_binary_size: 4000

    # -------------------------------------------------------------------------------
    # P. Remote Terminology Service (disabled by default)
    # -------------------------------------------------------------------------------
    # remote_terminology_service:
    #   all:
    #     system: "*"
    #     url: "https://tx.fhir.org/r4/"
    #   snomed:
    #     system: "http://snomed.info/sct"
    #     url: "https://tx.fhir.org/r4/"
    #   loinc:
    #     system: "http://loinc.org"
    #     url: "https://hapi.fhir.org/baseR4/"

    # -------------------------------------------------------------------------------
    # Q. Subscriptions (disabled by default)
    # -------------------------------------------------------------------------------
    # subscription:
    #   resthook_enabled: true
    #   websocket_enabled: false
    #   polling_interval_ms: 5000
    #   immediately_queued: false
    #   email:
    #     from: some@test.com
    #     host: google.com
    #     port:
    #     username:
    #     password:
    #     auth:
    #       startTlsEnable:
    #       startTlsRequired:
    #       quitWait:

    # -------------------------------------------------------------------------------
    # R. LastN (analytics)
    # -------------------------------------------------------------------------------
    # lastn_enabled: true
    
    # -------------------------------------------------------------------------------
    # S. Testers (webui)
    # -------------------------------------------------------------------------------
    tester:
      home:
        name: Local Tester
        server_address: 'http://localhost:8080/fhir'
        refuse_to_fetch_third_party_urls: false
        fhir_version: R4