* Add Elasticsearch configuration section to application.yaml
* Add configuration for reindexing resources upon search parameter change
* Add Elasticsearch client configuration for testing
* Update logback dependencies because of a security issue and enable resource filtering in pom.xml
* Add application name and tester configuration to application.yaml. Refactor hibernate properties
* Add custom Elasticsearch configuration to create ElasticsearchClient bean
* Add index prefix configuration for Elasticsearch indices
* Fix Elasticsearch URI format in test initialization
* Refactor ElasticsearchConfig for improved readability and code style consistency (spotless:apply)
* Refactor ElasticsearchConfig for improved readability and code style consistency (spotless:apply)
* Update index prefix in application.yaml for Elasticsearch configuration
* Enhance index prefix validation and add sanitization method for Elasticsearch index names
* Merged with master in upstream
* Refactor ElasticsearchBootSvcImpl and ElasticsearchConfig for improved readability (mvn spotless)
* Comment out custom_content_path in application.yaml for clarity
* - Refactor application.yaml for improved structure and readability;
- Add PostgresLucenePatientIT integration test; and
- Update testcontainers dependencies to avoid compatibility issues with newer Docker APIs.
* Refactor PostgresLucenePatientIT to use external configuration file for test properties
* Add integration tests for PostgreSQL and Elasticsearch with dynamic configuration
* Increase socket timeout in CdsHooksServletIT for improved stability during tests
* Remove deprecated tester configuration from application.yaml
* Added MCP support using SSE on http://localhost:8080/sse
* Reverted change that IntelliJ complains about
* Pre-rework
* Cleaned up the code a fair bit
* Renamed
* Renamed
* Running spotless
* Reuse FhirContext in result serialization to make MCP server work with R5
* Added support for transactions
* PoC tool for CDS Hooks
* some cleanup
* Upgrade of model protocol
* Added comments
* Removed field injection ... CDS to be changed to AutoConfig eventually
* Adjusted to new builder pattern
* Update src/main/java/ca/uhn/fhir/rest/server/MCPBridge.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* A bit of restructuring
* More rework
* Removing (suspected unnecessary) formatting
* Add more example doc
* Added a smoke- / passthrough-test
* Applied spotless
* Update src/main/java/ca/uhn/fhir/jpa/starter/mcp/RequestBuilder.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update src/main/java/ca/uhn/fhir/jpa/starter/mcp/RequestBuilder.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update src/main/java/ca/uhn/fhir/jpa/starter/mcp/ToolFactory.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update src/main/java/ca/uhn/fhir/rest/server/McpCdsBridge.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update src/main/java/ca/uhn/fhir/rest/server/McpCdsBridge.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Formatting
* Added some documentation
* spotless cares about MD?
* Reverting back to default values
* minor refinements
* Fixed CDS hooks configuration
* Fixed some wirings
* Readded missing elements
* getting closer to get test running again ...
* applying review
* Readded exclude
* Bumped spring-ai deps
* added agents file
* Updated according to review
---------
Co-authored-by: Ádám Z. Kövér <adamzkover@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Fixing up elastic for Spring Boot
* Adding class shadowing for issue reported on https://github.com/hapifhir/hapi-fhir/pull/7242
* Formatting
* corrected condition
* fix import
* fix2
* crappy fix3
* fix actuator endpoint
* Simplified expression
* Ironed out a few legacy issues
* more rework
* major overhaul
* Disabling invalid test
* Reverting back to defaults for text searches
* Added default hibernate settings from the EnvironmentHelper
* Formatting
* Added comment on class shadow
* Added missing default
* Added MCP support using SSE on http://localhost:8080/sse
* Reverted change that IntelliJ complains about
* Pre-rework
* Cleaned up the code a fair bit
* Renamed
* Renamed
* Running spotless
* Reuse FhirContext in result serialization to make MCP server work with R5
* Added support for transactions
* PoC tool for CDS Hooks
* some cleanup
* Upgrade of model protocol
* Added comments
* Removed field injection ... CDS to be changed to AutoConfig eventually
* Adjusted to new builder pattern
* Update src/main/java/ca/uhn/fhir/rest/server/MCPBridge.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* A bit of restructuring
* More rework
* Removing (suspected unnecessary) formatting
* Add more example doc
* Added a smoke- / passthrough-test
* Applied spotless
* Update src/main/java/ca/uhn/fhir/jpa/starter/mcp/RequestBuilder.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update src/main/java/ca/uhn/fhir/jpa/starter/mcp/RequestBuilder.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update src/main/java/ca/uhn/fhir/jpa/starter/mcp/ToolFactory.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update src/main/java/ca/uhn/fhir/rest/server/McpCdsBridge.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update src/main/java/ca/uhn/fhir/rest/server/McpCdsBridge.java
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Formatting
* Added some documentation
* spotless cares about MD?
* Reverting back to default values
* minor refinements
* Fixed CDS hooks configuration
* Fixed some wirings
* Revert "Fixed some wirings"
This reverts commit c9d3bc0b3b6756d7b15f5d2cf6100c99784fb868.
* Revert "Fixed CDS hooks configuration"
This reverts commit 67c4279100bf14432c164906235ea6348ee8af22.
---------
Co-authored-by: Ádám Z. Kövér <adamzkover@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* some cleanup
* results from mvn spotless:apply
* fix contructor --> constructor
* revert change to fix CdsHooksServletIT
* revert change to charts README.md
* bump chart version, required due to changes in README.md
* Bump to HAPI 7.5.0-SNAPSHOT
* Bump to latest HAPI version + fix config
* Bump to latest HAPI version + fix CR config + spotless
* Bump parent version to 7.5.4-SNAPSHOT
* Update to HAPI Release 7.6.0
---------
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
* Fixing prometheus so that it actually works. Also seems related to https://github.com/micrometer-metrics/micrometer/issues/5093
* cleaning up override
* Limiting exposure
* Added docs
* Added smoketest for prometheus endpoint
* Removing metrics and prometheus exposure by default
* Removing 'info'
Adding parameterized tests for endpoints
* Reintroduced 'info'
* Remove info
* Adjusted comment
* 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>
* Allow custom operations/providers to be added in the same way custom interceptors are currently loaded
* Add new property to documentation and default yaml file
* Add test for custom operation
unrequested changes: commons-logging dependency marked provided (to avoid redundant jar inclusion), removed unused imports in classes that were modified
* Affected Issue(s): #611
What this commit has achieved:
1. MDM requires an implementation of `INicknameSvc`, it was instantiated
in `NicknameServiceConfig`
The error message regarding this was:
```
APPLICATION FAILED TO START
Description:
Parameter 2 of method matcherFactory in
ca.uhn.fhir.jpa.mdm.config.MdmCommonConfig required a bean of type
'ca.uhn.fhir.jpa.nickname.INicknameSvc' that could not be found.
Action:
Consider defining a bean of type 'ca.uhn.fhir.jpa.nickname.INicknameSvc'
in your configuration.
```
2. MDM requires the subscription of type message
The error message regarding this was:
```
2023-12-01 11:34:03
org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'mdmSubmitterInterceptorLoader': Invocation of init
method failed; nested exception is
ca.uhn.fhir.context.ConfigurationException: HAPI-2421: MDM requires
Message Subscriptions to be enabled in the Storage Settings
```
* Affected Issue(s): #611
What this commit has achieved:
1. Added Integration Test for future-proof
