update from upstream #1
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* Add PostgreSQL connect route * Add pg pwd and external compose ports
* Create self-signed certs and stores * Added SSL support only for external servers
* Added threaded NATS subscriber startup and retries
* sample file checkpoint * working resource transaction bundle. Started on CSV file * simplifying etl samples to focus on US Core practitioner data
* Support for NAACCR Pathology Lab Reporting and Cancer Registry standards Support for NAACCR Pathology Lab Reporting and Cancer Registry standards. NAACCR is a subprotocol of HL7 used to transmit pathology reports from LIS/APLIS lab systems. NAACCR XML is the standard for representing cancer registry incidents based on SEER and CAP organizations. This commit extends the existing HL7 route to detect these NAACCR messages as well as adds additional HL7 over HTTP endpoint. Also exposes cancer registry GET endpoint to pull NAACCR formatted messages. * updated logging * code clean-up * added logging and content-based routing for NAACCR messages * updates to report processing * added unit test and sample messages * update processor to extract narrative report diag and site attributes * updated NAACCR processor to include synoptic reports, updated test case, and routes * fixed to use dynamic property for datastore uri * code clean-up * added more support to CAP eCC items * more clean-up and bug fix on parsing tumor site segment * remove debug code * fix primary site and site finding * updated Naaccr Xml Converter and body encoding * cleaned up code , refactored constants * proposed exchange properties to message metadata snippet * updated unit tests * changed use of String.isBlank to back-level Java version equivalent (trim + isEmpty) addresses back-level Java compile break * removed exception stack trace * removed blank line
* Updated .env to use kafdrop-alpine * Created an alpine image for connect
* checkpoint with draft documentation * checkpoint * ETL Route implementation with tests * PR feedback * test case updates * updating postman collection
* Generalize NLP analysis route * Add unit test and kafka consumer route enablement toggle • Add unit test case • Add prop to enable/disable the kafka consumer route • Extract kafka topics into a property setting * consolidate choice when stanzas * Incorporate code cleanliness feedback from PR * Move fhir attachment processing from dsl to a bean * Add success/error nlp response handling * Update LinuxForHealth Examples.postman_collection.json * Add missing fhir DocumentReference postman endpoint * Add DiagnosticReport attachment processing
* Add fhir api location response header Initial commit to dynamically construct the get url for retrieving the persisted fhir resource * Update FhirR4RouteBuilder.java Cleanup import statements * Fix FhirR4RouteTest unit test failure * Add kong ssl port env vars and lfh-customer loc header * Make LFHMetadataLocation path response header relative * Refactor lfh location header setting and add unit tests * Update LinuxForHealthStoreAndNotifyTest.java * Remove kong ssl port env var settings in compose ymls The lfh location header is relative, so no need for ascertaining kong port * Condense header processing logic
* Update request for single optional external fhir backend Fhir response is returned from lfh post api when an external fhir server is configured, otherwise the original lfh message is returned. * Revise ext fhir test to expect the fhir response The mockResult expectations need to be set prior to fluentTemplate.send, otherwise they don't take affect. I moved the expectation checks accordingly and revised them to the proper checks for the ext fhir route. * Revert test log settings from debug to info * Make ext fhir server property singular and condense producer req
* fix for x12 transaction split with improvements for x12 route * restoring logging values
* Created relative URL in Orthanc data payload * Removed external host IP var * Refactored configure-kong.sh
* adding LFH_CONNECT_X12_EXTERNAL_URI * adding LFH_CONNECT_X12_EXTERNAL_URI to docker compose pi configuration
* initial apple carekit support * Updated processor to load JSONObject from cached original message
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