LOOP BMIP FHIR to SPHN Mapping

FHIR to SPHN mappings for LOOP BMIP using FHIR Mapping Language (FML)

• Mappings: maps

StructureDefinitions for the target LOOP schema is defined using FHIR Shorthand (FSH)

• FSH: input/fsh/LogicalModel.fsh

Install

• Install SUSHI from https://github.com/FHIR/sushi
• For building the IG, jekyll is required:
  • sudo apt install jekyll
• Optional VS Code extensions for development:
  • FHIR Shorthand
  • REST Client

An FML engine is required like HAPI-FHIR Validator Cli or Matchbox (recommended)

Recommended versions: Use at least 6.5.0 for HAPI-FHIR Validator Cli and 4.0.1 for Matchbox or later. These releases contain critical performance improvements required to transform large amount of data (see hapifhir/org.hl7.fhir.core#1704 / ahdis/matchbox#362) and corresponding issues #1703 / #1699

HAPI-FHIR Validator Cli

• Download validator:
  • wget https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar

Matchbox

• Requires JDK 21 and maven
  • sudo apt install openjdk-21-jdk
  • sudo apt install maven
• Clone matchbox

cd ${HOME}
git clone https://github.com/ahdis/matchbox.git

StructureDefinitions

Generate StructureDefinitions (unshorten FSH):

sushi build

Build Implementation Guide (IG)

./_updatePublisher.sh
./_genonce.sh

Running transformations using Validator Cli

Compile maps

OUT_DIR="temp/map"
mkdir -p ${OUT_DIR}
for f in $(ls maps/*.map) ; do
    BASE=$(basename ${f} .map)
    java -jar validator_cli.jar -ig ${f} \
        -compile http://research.balgrist.ch/fhir2sphn/StructureMap/${BASE} \
        -version 4.0 -output ${OUT_DIR}/${BASE}.xml
done

Execute a transformation

Transform input data testdata/pat.json:

java -jar validator_cli.jar testdata/pat.json \
    -transform http://research.balgrist.ch/fhir2sphn/StructureMap/BundleToLoopSphn \
    -version 4.0 -ig ${OUT_DIR}/ -ig ./fsh-generated/resources \
    -output temp/result.json

Validate the result

Validate the resulting temp/result.json against the LogicalModel:

java -jar validator_cli.jar temp/result.json \
    -version 4.0 -ig ./fsh-generated/resources

Running transformations using Matchbox

Run local matchbox server:

cd matchbox/matchbox-server
mvn clean install -DskipTests spring-boot:run -Dspring-boot.run.jvmArguments="-Xmx4g" \
	-Dspring-boot.run.directories=../../LOOP_FHIR2SPHN/output \
	-Dspring-boot.run.arguments=--spring.config.additional-location=file:../../LOOP_FHIR2SPHN/with-preload/application.yaml

Note: After updating the StructureDefinitions, the database needs to be cleared to force re-loading of the IG package (output/package.tgz):

rm -rf matchbox/matchbox-server/database

Compile maps / execute transformation

• POST maps and execture transformation using REST against local matchbox server:
  • See transform.http

Postprocessing

cat temp/result.json  | jq 'walk(if type == "object" then with_entries(.key = (if .key == "reference" then "id" else .key end)) else . end)' | jq 'walk(if type == "object" then with_entries(.key = (if .key != "id" and .key != "iri" and .key != "termid" and .key != "content" and .key != "target_concept" then "sphn:" else "" end ) + .key) else . end)'