6.4. Do the mapping¶

If not further mentioned, the paths are relative to fhir-bridge/src/main/java/org/ehrbase/fhirbridge ## Prepare setup

6.4.1. Create new branch¶

Each change to the FHIR bridge should have a ticket created, explaining the change. Create a new feature branch with ticket number like: feature/123_awesome_new_feature, where 123 stands for the issue number

# optional: make a new checkout
git clone git@github.com:ehrbase/fhir-bridge.git
# default:
cd fhir-bridge
git checkout -b [BRANCH-NAME]
# At the first push:
git push -u origin [BRANCH-NAME]
# For later pushes:
git push

6.4.2. Start docker¶

Start docker, the erhdb and the fhirdb if they don’t already run. For example (Birgit 2020-10-16)

docker rm ehrdb
docker rm ehrbase
docker run --name ehrdb --network ehrbase-net -e POSTGRES_PASSWORD=postgres -d -p 5432:5432 ehrbase/ehrbase-postgres:latest
docker run --name ehrbase --network ehrbase-net -d -p 8080:8080 -e DB_URL=jdbc:postgresql://ehrdb:5432/ehrbase -e DB_USER=ehrbase -e DB_PASS=ehrbase -e AUTH_TYPE=none -e SYSTEM_ALLOW_TEMPLATE_OVERWRITE=true -e SERVER_NODENAME=local.ehrbase.org ehrbase/ehrbase:latest
docker run -p 9999:5432 --name fhir-bridge -e POSTGRES_PASSWORD=fhir_bridge -e POSTGRES_USER=fhir_bridge -d postgres

6.4.3. Build¶

Build the current fhir-bridge

mvn clean install

6.4.4. IDE¶

Load project into development environment

especially for eclipse: as a Maven project

6.4.4.1. Add external files¶

The following files must be copied into the respective target directories.

FHIR data structure (XML format)
- Target directory fhir-bridge/src/main/resources/profiles
- Source https://simplifier.net/ForschungsnetzCovid-19 (under Resources/Observation)
FHIR observation sample file (JSON format)
- Target directory fhir-bridge/src/test/resources/Observation
- Source https://simplifier.net/ForschungsnetzCovid-19/~resources?fhirVersion=R4&sortBy=RankScore_desc
- You can set a filter to the Examples
- Caution:
  - the profile must be a profile from simplifier-Covid 19, fitting to the profile you just downloaded
  - the profile must have a working UUID (like subject: { reference: Patient/07f602e0-579e-4fe3-95af-381728bf0d49 })
Operational template (OPT format)
- Target directory fhir-bridge/src/main/resources/opt
- Source http://88.198.146.13/ckm/projects/1246.152.26/resourcecentre (GECCO Core)
- Check the OPT in Pablos Tool: toolkit.cabolabs.com
Remember to check the downloaded files for content and syntax errors.
Here you can check your syntax
- Check for xml: https://xmllint.com/en
- Check for json: https://jsonlint.com/

6.4.4.2. Design the mapping¶

Design the mapping by looking for 1..1 in the Fhir-profile and the fields in the OPT.
Example https://drive.google.com/file/d/1naGVhto6efWfF2sDoO86pYTnaUiiMq3J/view?usp=sharing

6.4.5. Structure Definition (Enum)¶

copy the Fhir-Url from resources/profiles/[TEMPLATE].opt to fhir/Profile.java

<StructureDefinition xmlns="http://hl7.org/fhir">
  <url value="https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/body-height" />
  <name value="BodyHeight" />

if your FHIR-observation-sample-file contains an extension, add its Profile URL, too.
Add an entry in /config/util/OperationalTemplateData.java with the name of the opt-file and the template_id-value

# Koerpergroesse.opt
[...]
    <template_id>
        <value>Körpergröße</value>
    </template_id>

HEART_RATE("", "Koerpergroesse.opt", "Körpergröße"),

6.4.6. Use the SDK generator to create new classes from the operational template¶

(Windows example started from the path :code:`../openEHR_SDK/generator/target)

java
-jar generator-0.3.7.jar
-opt ../../../fhir-bridge/src/main/resources/opt/Atemfrequenz.opt
-out ../../../fhir-bridge/src/main/java
-package org.ehrbase.fhirbridge.opt

Linux example (only resource-opt needs to be adapted)

java -jar ../openEHR_SDK/generator/target/generator-0.3.7.jar -opt src/main/resources/opt/KlinischeFrailty.opt -out src/main/java/ -package org.ehrbase.fhirbridge.opt

Note: Ignore error message regarding missing language packages (temporary problem; TerminologyProvider).
Refresh project in the development environment
New classes and structures (example breathing rate)

$ opt/breathingfrequencycomposition
├── BreathrateComposition.java
├── BreathrateCompositionContainment.java
├── definition
    ├── RespiratoryRateObservation.java
    └── RespiratoryRateObservationContainment.java

            Structure Definition (Enum)

copy the Fhir-Url from resources/profiles/[TEMPLATE].opt to fhir/Profile.java

<StructureDefinition xmlns="http://hl7.org/fhir">
  <url value="https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/body-height" />
  <name value="BodyHeight" />

if your FHIR-observation-sample-file contains an extension, add its Profile URL, too.
Add an entry in /config/util/OperationalTemplateData.java with the name of the opt-file and the template_id-value

# Koerpergroesse.opt
[...]
    <template_id>
        <value>Körpergröße</value>
    </template_id>

HEART_RATE("", "Koerpergroesse.opt", "Körpergröße"),

6.4.7. Use the SDK generator to create new classes from the operational template¶

(Windows example started from the path :code:`../openEHR_SDK/generator/target)

java
-jar generator-0.3.7.jar
-opt ../../../fhir-bridge/src/main/resources/opt/Atemfrequenz.opt
-out ../../../fhir-bridge/src/main/java
-package org.ehrbase.fhirbridge.opt

Linux example (only resource-opt needs to be adapted)

java -jar ../openEHR_SDK/generator/target/generator-0.3.7.jar -opt src/main/resources/opt/KlinischeFrailty.opt -out src/main/java/ -package org.ehrbase.fhirbridge.opt

Note: Ignore error message regarding missing language packages (temporary problem; TerminologyProvider).
Refresh project in the development environment
New classes and structures (example breathing rate)

$ opt/breathingfrequencycomposition
├── BreathrateComposition.java
├── BreathrateCompositionContainment.java
├── definition
    ├── RespiratoryRateObservation.java
    └── RespiratoryRateObservationContainment.java