Update Clinical Reasoning plugin (#692)
* Reproducing issues with CR/HAPI cds-hooks processing * Add new $questionnaire operation * Update StarterIpsConfig.java * Update pom.xml * Fixes for configuration properties * Update VS Code launch properties * Fixes for CQL logging * Update pom.xml * Remove unused threaded option * Update to 7.1.7 * Fix some CR defaults * Update to new snapshot * Update pom.xml * Fix test settings * Do not make prefetch calls if all items are present * Add alternative application.yaml for CDS settings. * Add CdsHook tests and documentation * Comment out custom prefetch until it is more mature * Removal of DataEndpoint parameter is not longer needed * Fix debug logging setting being overwritten * Revert change * Remove unused class * Adding Rec10 Test * Disable test until fixed * fix tests --------- Co-authored-by: c-schuler <hoofschu@gmail.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
This commit is contained in:
Brenin Rhodes
GitHub
294
src/main/resources/cds.application.yaml
Normal file
294
src/main/resources/cds.application.yaml
Normal file
@@ -0,0 +1,294 @@
|
||||
#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:
|
||||
endpoints:
|
||||
web:
|
||||
exposure:
|
||||
include: "health,prometheus"
|
||||
spring:
|
||||
main:
|
||||
allow-circular-references: true
|
||||
allow-bean-definition-overriding: true
|
||||
flyway:
|
||||
enabled: false
|
||||
baselineOnMigrate: true
|
||||
fail-on-missing-locations: false
|
||||
datasource:
|
||||
#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.HapiFhirPostgres94Dialect
|
||||
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: true
|
||||
### 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: true
|
||||
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_CODESYSTEM_URL # AUTO, USE_VALIDATE_CODE_OPERATION, USE_CODESYSTEM_URL
|
||||
data:
|
||||
search_parameter_mode: USE_SEARCH_PARAMETERS # 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: OFF # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF
|
||||
|
||||
cdshooks:
|
||||
enabled: true
|
||||
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
|
||||
### 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
|
||||
# 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
|
||||
|
||||
# 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
|
||||
Reference in New Issue
Block a user