pull request

.gitignore

@@ -16,4 +16,7 @@ download
 src/server/tasks/card_game/result
 .dockerfile
 .dockerfile-cache
-analysis
+analysis
+configs/agents/openai-chat.yaml
+configs/agents/together-chat.yaml
+configs/agents/gemini-chat.yaml

MedAgentBench/application.yaml

@@ -0,0 +1,329 @@
+#Uncomment the "servlet" and "context-path" lines below to make the fhir endpoint available at /example/path/fhir instead of the default value of /fhir
+server:
+  #  servlet:
+  #    context-path: /example/path
+  port: 8080
+#Adds the option to go to eg. http://localhost:8080/actuator/health for seeing the running configuration
+#see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
+management:
+  #The following configuration will enable the actuator endpoints at /actuator/health, /actuator/info, /actuator/prometheus, /actuator/metrics. For security purposes, only /actuator/health is enabled by default.
+  endpoints:
+    enabled-by-default: false
+    web:
+      exposure:
+        include: 'health' # or e.g. '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:
+  main:
+    allow-circular-references: true
+  flyway:
+    enabled: false
+    baselineOnMigrate: true
+    fail-on-missing-locations: false
+  datasource:
+    url: 'jdbc:h2:/data/test_db;DB_CLOSE_DELAY=-1;AUTO_SERVER=TRUE'
+    #url: 'jdbc:h2:file:./target/database/h2'
+    #url: jdbc:h2:mem:test_mem
+    username: sa
+    password: null
+    driverClassName: org.h2.Driver
+    max-active: 15
+
+    # database connection pool size
+    hikari:
+      maximum-pool-size: 10
+  jpa:
+    properties:
+      hibernate.format_sql: false
+      hibernate.show_sql: false
+
+      #Hibernate dialect is automatically detected except Postgres and H2.
+      #If using H2, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
+      #If using postgres, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
+      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
+  #      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 or elastic
+      hibernate.search.enabled: false
+  ### lucene parameters
+#      hibernate.search.backend.type: lucene
+#      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiLuceneAnalysisConfigurer
+#      hibernate.search.backend.directory.type: local-filesystem
+#      hibernate.search.backend.directory.root: target/lucenefiles
+#      hibernate.search.backend.lucene_version: lucene_current
+  ### elastic parameters ===> see also elasticsearch section below <===
+#      hibernate.search.backend.type: elasticsearch
+#      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
+hapi:
+  fhir:
+    ### This flag when enabled to true, will avail evaluate measure operations from CR Module.
+    ### Flag is false by default, can be passed as command line argument to override.
+    cr:
+      enabled: false
+      caregaps:
+        reporter: "default"
+        section_author: "default"
+      cql:
+        use_embedded_libraries: true
+        compiler:
+          ### These are low-level compiler options.
+          ### They are not typically needed by most users.
+          # 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: REQUIRE # USE_IF_PRESENT, REQUIRE, IGNORE
+          valueset_expansion_mode: PERFORM_NAIVE_EXPANSION # AUTO, USE_EXPANSION_OPERATION, PERFORM_NAIVE_EXPANSION
+          valueset_membership_mode: USE_EXPANSION # AUTO, USE_VALIDATE_CODE_OPERATION, USE_EXPANSION
+          code_lookup_mode: USE_VALIDATE_CODE_OPERATION # AUTO, USE_VALIDATE_CODE_OPERATION, USE_CODESYSTEM_URL
+        data:
+          search_parameter_mode: FILTER_IN_MEMORY # AUTO, USE_SEARCH_PARAMETERS, FILTER_IN_MEMORY
+          terminology_parameter_mode: FILTER_IN_MEMORY #  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
+
+    ### This enables the swagger-ui at /fhir/swagger-ui/index.html as well as the /fhir/api-docs (see https://hapifhir.io/hapi-fhir/docs/server_plain/openapi.html)
+    openapi_enabled: true
+    ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5
+    fhir_version: R4
+    ### Flag is false by default. This flag enables runtime installation of IG's.
+    ig_runtime_upload_enabled: false
+    ### This flag when enabled to true, will avail evaluate measure operations from CR Module.
+
+    ### 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
+    ### enables the server to overwrite defaults on HTML, css, etc. under the url pattern of eg. /content/custom **
+    ### Folder with custom content MUST be named custom. If omitted then default content applies
+    #custom_content_path: ./custom
+    ### enables the server host custom content. If e.g. the value ./configs/app is supplied then the content
+    ### will be served under /web/app
+    #app_content_path: ./configs/app
+    ### 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
+    #    reloadExisting: false
+    #    installMode: STORE_AND_INSTALL
+    #      example not from registry
+    #      ips_1_0_0:
+    #        packageUrl: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
+    #        name: hl7.fhir.uv.ips
+    #        version: 1.0.0
+    #    supported_resource_types:
+    #      - Patient
+    #      - Observation
+    ##################################################
+    # Allowed Bundle Types for persistence (defaults are: COLLECTION,DOCUMENT,MESSAGE)
+    ##################################################
+    #    allowed_bundle_types: COLLECTION,DOCUMENT,MESSAGE,TRANSACTION,TRANSACTIONRESPONSE,BATCH,BATCHRESPONSE,HISTORY,SEARCHSET
+    #    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
+    ### tells the server to automatically append the current version of the target resource to references at these paths
+    #    auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
+    #    ips_enabled: false
+    #    default_encoding: JSON
+    #    default_pretty_print: true
+    #    default_page_size: 20
+    #    delete_expunge_enabled: true
+    #    enable_repository_validating_interceptor: true
+    #    enable_index_missing_fields: false
+    #    enable_index_of_type: true
+    #    enable_index_contained_resource: false
+    #    upliftedRefchains_enabled: true
+    #    resource_dbhistory_enabled: false
+    ###  !!Extended Lucene/Elasticsearch Indexing is still a experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
+    ###  more information here: https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
+    advanced_lucene_indexing: false
+    bulk_export_enabled: false
+    bulk_import_enabled: false
+    #    language_search_parameter_enabled: true
+    #    enforce_referential_integrity_on_delete: false
+    # This is an experimental feature, and does not fully support _total and other FHIR features.
+    #    enforce_referential_integrity_on_delete: false
+    #    enforce_referential_integrity_on_write: false
+    #    etag_support_enabled: true
+    #    expunge_enabled: true
+    #    client_id_strategy: ALPHANUMERIC
+    #    server_id_strategy: SEQUENTIAL_NUMERIC
+    #    fhirpath_interceptor_enabled: false
+    #    filter_search_enabled: true
+    #    graphql_enabled: true
+    narrative_enabled: false
+    mdm_enabled: false
+    mdm_rules_json_location: "mdm-rules.json"
+    #    local_base_urls:
+    #      - https://hapi.fhir.org/baseR4
+    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/*
+    #    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:
+        - '*'
+
+    # Search coordinator thread pool sizes
+    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.
+    search_prefetch_thresholds: 13,503,2003,-1
+
+    # comma-separated package names, will be @ComponentScan'ed by Spring to allow for creating custom Spring beans
+    #custom-bean-packages:
+
+    # comma-separated list of fully qualified interceptor classes. 
+    # classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages', 
+    # or will be instantiated via reflection using an no-arg contructor; then registered with the server  
+    #custom-interceptor-classes:  
+
+    # comma-separated list of fully qualified provider classes. 
+    # classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages', 
+    # or will be instantiated via reflection using an no-arg contructor; then registered with the server  
+    #custom-provider-classes:  
+
+    # Threadpool size for BATCH'ed GETs in a bundle.
+    #    bundle_batch_pool_size: 10
+    #    bundle_batch_pool_max_size: 50
+
+    #    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
+    inline_resource_storage_below_size: 4000
+#    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
+#    store_resource_in_lucene_index_enabled: true
+###  This is configuration for normalized quantity search 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