446 lines
18 KiB
YAML
446 lines
18 KiB
YAML
# -------------------------------------------------------------------------------------
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# Server & Spring Boot
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# -------------------------------------------------------------------------------------
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server:
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# Uncomment to serve FHIR under a non-default context path (e.g., /example/path/fhir)
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# servlet:
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# context-path: /example/path
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port: 8080
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tomcat:
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# allow | as a separator in URLs
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relaxed-query-chars: "|"
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management:
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# Actuator endpoints: only /actuator/health exposed by default
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endpoints:
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enabled-by-default: false
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web:
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exposure:
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include: "health" # or "info,health,prometheus,metrics" or "*" for all
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endpoint:
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info:
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enabled: true
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metrics:
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enabled: true
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health:
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enabled: true
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probes:
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enabled: true
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group:
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liveness:
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include: [ "livenessState", "readinessState" ]
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prometheus:
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enabled: true
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prometheus:
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metrics:
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export:
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enabled: true
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spring:
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# -------------------------------------------------------------------------------
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# A. Spring AI — Model Context Protocol (MCP)
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# -------------------------------------------------------------------------------
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ai:
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# Run e.g. `npx @modelcontextprotocol/inspector` and connect to http://localhost:8080/mcp/messages using Streamable HTTP
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# Add the following to the MCP server settings file in e.g. cursor or claude (Desktop applications) for local debugging:
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# cursor:
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# {
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# "mcpServers": {
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# "hapi": {
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# "url": "http://localhost:8080/mcp/messages"
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# }
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# }
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# }
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# or claude:
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# {
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# "mcpServers": {
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# "hapi": {
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# "command": "npx",
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# "args": [
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# "mcp-remote@latest",
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# "http://localhost:8080/mcp/messages"
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# ]
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# }
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# }
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# }
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mcp:
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server:
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name: FHIR MCP Server
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version: 1.0.0
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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."
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enabled: true
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streamable-http:
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mcp-endpoint: /mcp/messages
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# -------------------------------------------------------------------------------
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# B. Core Spring
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# -------------------------------------------------------------------------------
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main:
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allow-bean-definition-overriding: false
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allow-circular-references: true
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autoconfigure:
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# This exclude is only needed for setups not using Elasticsearch where the elasticsearch sniff is not needed.
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exclude: org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration
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flyway:
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enabled: false
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baseline-on-migrate: true
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fail-on-missing-locations: false
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datasource:
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# url: "jdbc:h2:file:./target/database/h2"
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url: jdbc:h2:mem:test_mem
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username: sa
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password: null
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driver-class-name: org.h2.Driver
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# max-active: 15 # (ignored with HikariCP; use hikari.maximum-pool-size)
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hikari:
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maximum-pool-size: 10
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jpa:
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properties:
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hibernate:
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format_sql: false
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show_sql: false
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# Hibernate dialect is auto-detected except for H2/Postgres.
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# If using H2: ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
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# If using Postgres: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
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dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
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# --- Optional Hibernate DDL & tuning (commented out from source) ---
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hbm2ddl:
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auto: update
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jdbc:
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batch_size: 20
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cache:
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use_query_cache: false
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use_second_level_cache: false
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use_structured_entries: false
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use_minimal_puts: false
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# --- Hibernate Search (Lucene/Elasticsearch) ---
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search:
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enabled: false
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# Lucene backend (default example)
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# backend:
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# type: lucene
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# analysis:
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# configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiLuceneAnalysisConfigurer
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# directory:
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# type: local-filesystem
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# root: target/lucenefiles
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# lucene_version: lucene_current
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# Elasticsearch backend (alternative) — see also hapi.fhir.elasticsearch section in docs
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# backend:
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# type: elasticsearch
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# analysis:
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# configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
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# -------------------------------------------------------------------------------------
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# HAPI FHIR — grouped by domain
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# -------------------------------------------------------------------------------------
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hapi:
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fhir:
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# -------------------------------------------------------------------------------
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# A. Core Server & API
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# -------------------------------------------------------------------------------
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openapi_enabled: true # Swagger UI at /fhir/swagger-ui/index.html; API docs at /fhir/api-docs
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fhir_version: R4 # DSTU2 | DSTU3 | R4 | R5
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# use_apache_address_strategy: false
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# use_apache_address_strategy_https: false
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# custom_content_path: ./custom # folder name must be 'custom'
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# app_content_path: ./configs/app # served under /web/app
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# server_address: http://hapi.fhir.org/baseR4
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# defer_indexing_for_codesystems_of_size: 101
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# -------------------------------------------------------------------------------
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# B. Implementation Guides (IG) & Package Install
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# -------------------------------------------------------------------------------
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ig_runtime_upload_enabled: false
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# validate_resource_status_for_package_upload: false # default true
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# install_transitive_ig_dependencies: true
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# implementationguides:
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# swiss:
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# name: swiss.mednet.fhir
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# version: 0.8.0
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# reloadExisting: false
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# installMode: STORE_AND_INSTALL
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# ips_1_0_0:
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# packageUrl: https://costateixeira.github.io/smart-ips-pilgrimage-fulltest/package.tgz
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# name: smart.who.int.ips-pilgrimage-test
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# version: 0.1.0
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# installMode: STORE_AND_INSTALL
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# additionalResourceFolders:
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# - example
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# - example2
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# supported_resource_types:
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# - Patient
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# - Observation
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# allowed_bundle_types: COLLECTION,DOCUMENT,MESSAGE,TRANSACTION,TRANSACTIONRESPONSE,BATCH,BATCHRESPONSE,HISTORY,SEARCHSET
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# -------------------------------------------------------------------------------
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# C. Clinical Reasoning / CQL / Care Gaps / CDS Hooks
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# -------------------------------------------------------------------------------
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cr:
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enabled: false # exposes Clinical Reasoning operation endpoints
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caregaps:
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reporter: "default"
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section_author: "default"
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terminologyServerClientSettings:
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maxRetryCount: 3
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retryIntervalMillis: 1000
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timeoutSeconds: 30
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socketTimeout: 60
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cql:
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use_embedded_libraries: true
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compiler:
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# low-level compiler options (typically not needed)
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# validate_units: true
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# verify_only: false
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# compatibility_level: "1.5"
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error_level: Info
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signature_level: All
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# analyze_data_requirements: false
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# collapse_data_requirements: false
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# translator_format: JSON
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# enable_date_range_optimization: true
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enable_annotations: true
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enable_locators: true
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enable_results_type: true
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enable_detailed_errors: true
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# disable_list_traversal: false
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# disable_list_demotion: false
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# enable_interval_demotion: false
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# enable_interval_promotion: false
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# disable_method_invocation: false
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# require_from_keyword: false
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# disable_default_model_info_load: false
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runtime:
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debug_logging_enabled: false
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# enable_validation: false
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# enable_expression_caching: true
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terminology:
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valueset_preexpansion_mode: REQUIRE # USE_IF_PRESENT | REQUIRE | IGNORE
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valueset_expansion_mode: PERFORM_NAIVE_EXPANSION # AUTO | USE_EXPANSION_OPERATION | PERFORM_NAIVE_EXPANSION
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valueset_membership_mode: USE_EXPANSION # AUTO | USE_VALIDATE_CODE_OPERATION | USE_EXPANSION
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code_lookup_mode: USE_VALIDATE_CODE_OPERATION # AUTO | USE_VALIDATE_CODE_OPERATION | USE_CODESYSTEM_URL
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data:
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search_parameter_mode: USE_SEARCH_PARAMETERS # AUTO | USE_SEARCH_PARAMETERS | FILTER_IN_MEMORY
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terminology_parameter_mode: FILTER_IN_MEMORY # AUTO | USE_VALUE_SET_URL | USE_INLINE_CODES | FILTER_IN_MEMORY
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profile_mode: DECLARED # ENFORCED | DECLARED | OPTIONAL | TRUST | OFF
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cdshooks:
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enabled: false
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clientIdHeaderName: client_id
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# -------------------------------------------------------------------------------
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# D. Search & Indexing
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# -------------------------------------------------------------------------------
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# NOTE: Extended Lucene/Elasticsearch indexing is experimental.
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# See https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
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advanced_lucene_indexing: false
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search_index_full_text_enabled: false
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# language_search_parameter_enabled: true
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# upliftedRefchains_enabled: true
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# index_storage_optimized: false
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# enable_index_missing_fields: false
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# enable_index_of_type: true
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# enable_index_contained_resource: false
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# store_resource_in_lucene_index_enabled: true
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# -------------------------------------------------------------------------------
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# E. Bulk Operations
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# -------------------------------------------------------------------------------
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bulk_export_enabled: false
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bulk_import_enabled: false
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# -------------------------------------------------------------------------------
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# F. Write / Delete / Integrity
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# -------------------------------------------------------------------------------
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# allow_cascading_deletes: true
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# allow_contains_searches: true
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# allow_external_references: true
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# allow_multiple_delete: true
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# allow_override_default_search_params: true
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# auto_create_placeholder_reference_targets: false
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# mass_ingestion_mode_enabled: false
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# auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
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# client_id_strategy: ALPHANUMERIC
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# server_id_strategy: SEQUENTIAL_NUMERIC
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# enforce_referential_integrity_on_delete: false
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# enforce_referential_integrity_on_write: false
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# etag_support_enabled: true
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# expunge_enabled: true
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# fhirpath_interceptor_enabled: false
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# filter_search_enabled: true
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# graphql_enabled: true
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# Thread pool configuration for maintenance operations
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# Defaults to Runtime.getRuntime().availableProcessors() if not specified
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# reindex_thread_count: 4 # Number of threads to use for reindex operations
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# expunge_thread_count: 4 # Number of threads to use for expunge operations
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# mark_resources_for_reindexing_upon_search_parameter_change: false
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# -------------------------------------------------------------------------------
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# G. Narrative & Validation
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# -------------------------------------------------------------------------------
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narrative_enabled: false
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# validation:
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# requests_enabled: true
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# responses_enabled: true
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# -------------------------------------------------------------------------------
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# H. MDM (Master Data Management)
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# -------------------------------------------------------------------------------
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mdm_enabled: false
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mdm_rules_json_location: "mdm-rules.json"
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# userRequestRetryVersionConflictsInterceptorEnabled: false
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# -------------------------------------------------------------------------------
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# I. Terminology / ValueSet Expansion
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# -------------------------------------------------------------------------------
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# pre_expand_value_sets: true
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# enable_task_pre_expand_value_sets: true
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# pre_expand_value_sets_default_count: 1000
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# pre_expand_value_sets_max_count: 1000
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# maximum_expansion_size: 1000
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logical_urls:
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- http://terminology.hl7.org/*
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- https://terminology.hl7.org/*
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- http://snomed.info/*
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- https://snomed.info/*
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- http://unitsofmeasure.org/*
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- https://unitsofmeasure.org/*
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- http://loinc.org/*
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- https://loinc.org/*
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# -------------------------------------------------------------------------------
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# J. Partitioning & Multitenancy
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# -------------------------------------------------------------------------------
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# partitioning:
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# allow_references_across_partitions: false
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# partitioning_include_in_search_hashes: false
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# default_partition_id: 0
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# database_partition_mode_enabled: true
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# patient_id_partitioning_mode: true
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# request_tenant_partitioning_mode: false
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# -------------------------------------------------------------------------------
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# K. CORS
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# -------------------------------------------------------------------------------
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cors:
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allow_Credentials: true
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allowed_origin:
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- "*"
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# -------------------------------------------------------------------------------
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# L. Search Orchestration
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# -------------------------------------------------------------------------------
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search-coord-core-pool-size: 20
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search-coord-max-pool-size: 100
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search-coord-queue-capacity: 200
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# Search Prefetch Thresholds.
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# This setting sets the number of search results to prefetch. For example, if this list
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# is set to [100, 1000, -1] then the server will initially load 100 results and not
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# attempt to load more. If the user requests subsequent page(s) of results and goes
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# past 100 results, the system will load the next 900 (up to the following threshold of 1000).
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# The system will progressively work through these thresholds.
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# A threshold of -1 means to load all results. Note that if the final threshold is a
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# number other than -1, the system will never prefetch more than the given number.
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# CSV list; -1 as final value means "all"
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search_prefetch_thresholds: 13,503,2003,-1
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# -------------------------------------------------------------------------------
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# M. Extensibility (custom beans / interceptors / providers)
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# -------------------------------------------------------------------------------
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# comma-separated package names, will be @ComponentScan'ed by Spring to allow for creating custom Spring beans
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# custom-bean-packages:
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# custom-interceptor-classes:
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# custom-provider-classes:
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# store_meta_source_information: NONE
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# bundle_batch_pool_size: 10
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# bundle_batch_pool_max_size: 50
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# -------------------------------------------------------------------------------
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# N. Logging
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# -------------------------------------------------------------------------------
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# logger:
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# error_format: "ERROR - ${requestVerb} ${requestUrl}"
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# format: >-
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# Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
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# Operation[${operationType} ${operationName} ${idOrResourceName}]
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# UA[${requestHeader.user-agent}] Params[${requestParameters}]
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# ResponseEncoding[${responseEncodingNoDefault}]
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# log_exceptions: true
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# name: fhirtest.access
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# -------------------------------------------------------------------------------
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# O. Storage / Pagination / Caching
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# -------------------------------------------------------------------------------
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# max_binary_size: 104857600
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# max_page_size: 200
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# retain_cached_searches_mins: 60
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# reuse_cached_search_results_millis: 60000
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# validation:
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# requests_enabled: true
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# responses_enabled: true
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# binary_storage_enabled: true
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# binary_storage_mode: FILESYSTEM
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# binary_storage_filesystem_base_directory: /binstore
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# When binary_storage_mode is FILESYSTEM and this value is not set,
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# the starter defaults to 102400 bytes so smaller binaries stay inline.
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inline_resource_storage_below_size: 4000
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# -------------------------------------------------------------------------------
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# P. Remote Terminology Service (disabled by default)
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# -------------------------------------------------------------------------------
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# remote_terminology_service:
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# all:
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# system: "*"
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# url: "https://tx.fhir.org/r4/"
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# snomed:
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# system: "http://snomed.info/sct"
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# url: "https://tx.fhir.org/r4/"
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# loinc:
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# system: "http://loinc.org"
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# url: "https://hapi.fhir.org/baseR4/"
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# -------------------------------------------------------------------------------
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# Q. Subscriptions (disabled by default)
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# -------------------------------------------------------------------------------
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# subscription:
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# resthook_enabled: true
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# websocket_enabled: false
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# polling_interval_ms: 5000
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# immediately_queued: false
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# email:
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# from: some@test.com
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# host: google.com
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# port:
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# username:
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# password:
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# auth:
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# startTlsEnable:
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# startTlsRequired:
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# quitWait:
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# -------------------------------------------------------------------------------
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# R. LastN (analytics)
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# -------------------------------------------------------------------------------
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# lastn_enabled: true
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# -------------------------------------------------------------------------------
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# S. Testers (webui)
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# -------------------------------------------------------------------------------
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tester:
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home:
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name: Local Tester
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server_address: 'http://localhost:8080/fhir'
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refuse_to_fetch_third_party_urls: false
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fhir_version: R4 |