(HAPI) Terminology Server - UK SNOMED CT Import

(Kev Mayfield) #1

Instructions for setting up a HAPI server can be found at https://github.com/KevinMayfield/Jorvik/blob/master/Documentation/UK%20HAPI%20FHIR%20Server%20Instructions%201v01.docx
This also includes early work on a regional set of UK FHIR ValueSets (based on NHS ITK Reference data for SNOMED, HL7 v2 and v3)

To import SNOMED CT (RF2) HAPI needs to be configured as a terminology server. This is done by adding a Terminology Provider to your JPAServer configuration e.g.


(See line 146 in https://github.com/KevinMayfield/Jorvik/blob/master/hapi-fhir-jpaserver/src/main/java/uk/co/mayfieldis/hapifhir/jpa/demo/JpaServerDemo.java)
The upload is run by the hapi command line tools. Instructions for downloading can be found here http://hapifhir.io/doc_cli.html

In the UK(/England) the UK SNOMED CT Clinical Edition (RF2) can be found on TRUD
You may need to both register and subscribe to TRUD to get access to the download. Place the downloaded zip file in a suitable location. (The import was tested against SNOMEDCT2_21.0.0_20160401000001 dated 1st April 2016).
To run the import execute the following command at a command prompt

java -jar hapi-fhir-cli.jar upload-terminology -d c:\hapi-fhir\uk_sct2clfull_21.0.0_20160401000001.zip -f dstu3 -t http://localhost:8080/hapi-fhir-jpaserver/baseStu3 -u http://snomed.info/sct

-t parameter is the base url of your HAPI server
-d is the full path of your SNOMED CT RF2 zipfile

The import will take a while and will continue processing after the cli tool has finished. [The CLI tool finishes after it has loaded the data to the HAPI Server, the server then adds the data to the database]. On SQL Server the database load can be checked by running this query:

Select count(*) from dbo.TRM__CONCEPT

Syntax on other SQL systems should be similar.

Test the load has worked by executing the following query$lookup?system=http://snomed.info/sct&code=209629006

This should return


“valueString”:“Complete tear, knee, anterior cruciate ligament (disorder)”