### Verify Keycloak Startup Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/02_testing/security_tests.rst Example output indicating that the Keycloak service has successfully started. ```bash Keycloak 10.0.2 (WildFly Core 11.1.1.Final) started in 11390ms - Started 591 of 889 services (606 services are lazy, passive or on-demand) ``` -------------------------------- ### Install Docker on Linux Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/gettingstarted.rst Install the Docker engine using apt-get. ```bash sudo apt-get install docker ``` -------------------------------- ### Install IntelliJ IDEA on Linux Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/gettingstarted.rst Install the IntelliJ IDEA community edition via snap. ```bash sudo snap install intellij-idea-community --classic ``` -------------------------------- ### Linux Installation and Build Commands Source: https://github.com/ehrbase/documentation/blob/master/README.md Commands for installing Sphinx and building documentation on Linux systems. ```bash $ apt install python3-sphinx $ make html ``` ```bash $ pip install "Sphinx=2.4.3" $ python -m pip list | grep Sphinx $ make html ``` ```bash $ pip install sphinx_rtd_theme $ python -m pip list | grep sphinx $ make html ``` -------------------------------- ### Install Test Dependencies Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/02_testing/00_integration_tests.rst Navigate to the tests directory and install required Python packages. ```bash cd tests pip install -r requirements.txt ``` -------------------------------- ### Start Keycloak with Mounted Volume Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/02_testing/security_tests.rst Initializes a Keycloak container with a volume mount for configuration persistence. This setup uses the embedded H2 database, suitable for testing environments. ```bash docker run -d --name keycloak \ -p 8081:8080 \ -v $(pwd)/exported-keycloak-config:/restore-keycloak-config \ -e KEYCLOAK_USER=admin \ -e KEYCLOAK_PASSWORD=admin \ jboss/keycloak:10.0.2 ``` ```bash docker run -d --name keycloak \ -p 8081:8080 \ -v $(pwd)/exported-keycloak-config:/restore-keycloak-config \ -e KEYCLOAK_USER=admin \ -e KEYCLOAK_PASSWORD=admin \ jboss/keycloak:10.0.2 ``` ```bash docker run -d --name keycloak \ -p 8081:8080 \ -v $(pwd):/workspace \ -e KEYCLOAK_USER=admin \ -e KEYCLOAK_PASSWORD=admin \ jboss/keycloak:10.0.2 ``` -------------------------------- ### Install AdoptOpenJDK on Linux Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/gettingstarted.rst Commands to install the required Java Development Kit and JRE on Linux systems. ```bash sudo apt-get install adoptopenjdk-11-hotspot sudo apt-get install adoptopenjdk-11-hotspot-jre ``` -------------------------------- ### Install Sphinx HTML Domain Source: https://github.com/ehrbase/documentation/blob/master/README.md Install the sphinxcontrib-httpdomain extension required for building the documentation. ```bash pip install sphinxcontrib-httpdomain ``` -------------------------------- ### Basic COMPOSITION Mapping Example Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A minimal example of a COMPOSITION mapping structure. ```json { "conformance-ehrbase.de.v0/language|code": "en", "conformance-ehrbase.de.v0/language|terminology": "ISO_639-1", "conformance-ehrbase.de.v0/territory|code": "US", "conformance-ehrbase.de.v0/territory|terminology": "ISO_3166-1", "conformance-ehrbase.de.v0/category|code": "433", "conformance-ehrbase.de.v0/category|value": "event", "conformance-ehrbase.de.v0/category|terminology": "openehr", "conformance-ehrbase.de.v0/context/start_time": "2021-12-21T14:19:31.649613+01:00", "conformance-ehrbase.de.v0/context/setting|code": "238", "conformance-ehrbase.de.v0/context/setting|value": "other care", "conformance-ehrbase.de.v0/context/setting|terminology": "openehr", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|magnitude": 65.9, "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|unit": "unit", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/time": "2021-12-21T16:02:58.0094262+01:00", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/language|code": "en", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/language|terminology": "ISO_639-1", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/encoding|code": "UTF-8", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/encoding|terminology": "IANA_character-sets", "conformance-ehrbase.de.v0/composer|name": "Silvia Blake" } ``` -------------------------------- ### Start Database Container Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/gettingstarted.rst Run the PostgreSQL database container for audit logs. ```bash docker run --name fhirdb -e POSTGRES_PASSWORD=fhir_bridge -e POSTGRES_USER=fhir_bridge -d -p 9999:5432 postgres ``` -------------------------------- ### Install Sphinx RTD Theme Source: https://github.com/ehrbase/documentation/blob/master/README.md Install the Read the Docs theme if a ModuleNotFoundError occurs. ```bash pip install sphinx_rtd_theme ``` -------------------------------- ### Start Docker containers Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/ManualMappingInstruction.rst Commands to remove existing containers and start the required EHRbase and PostgreSQL instances for the FHIR bridge. ```bash 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 ``` -------------------------------- ### OBSERVATION Flat Data Path Examples Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Example key-value pairs representing flat data paths for an OBSERVATION archetype. ```json "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:0|name": "Dr. Marcus Johnson", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:0|id": "199", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:0|id_namespace": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:0|id_scheme": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:1|function": "performer", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:1|mode": "not specified", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:1|name": "Lara Markham", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:1|id": "198", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:1|id_namespace": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_other_participation:1|id_scheme": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_guideline_id|type": "GUIDELINE", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_guideline_id|namespace": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_guideline_id|id": "3445", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_guideline_id|id_scheme": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_work_flow_id|type": "WORKFLOW", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_work_flow_id|namespace": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_work_flow_id|id": "335645", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_work_flow_id|id_scheme": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_uid":"9fcc1c70-9349-444d-b9cb-8fa817697f5e", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_link:0|type": "problem", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_link:0|meaning": "problem related note", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_link:0|target": "ehr://ehr.network/347a5490-55ee-4da9-b91a-9bba710f730e", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/originating_system_audit|version_id": "final", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/originating_system_audit|system_id": "orig", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/original_content": "Hello world!", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/original_content|formalism": "text/plain" ``` -------------------------------- ### TERM_MAPPING JSON Examples Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Examples showing the structure of TERM_MAPPING, including optional purpose fields. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0|match": "=", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0/target|terminology": "SNOMED-CT", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0/target|code": "21794005" } ``` ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0|match": "=", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0/target|terminology": "SNOMED-CT", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0/target|code": "21794005", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0/purpose|terminology": "openehr", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0/purpose|code": "671", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_mapping:0/purpose|value": "research study" } ``` -------------------------------- ### Example content of run_local_tests.sh Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/02_testing/00_integration_tests.rst A sample configuration for the shell script used to execute contribution tests. ```bash robot --include contribution \ --exclude TODO -e future -e obsolete -e libtest \ --loglevel TRACE \ --noncritical not-ready \ --flattenkeywords for \ --flattenkeywords foritem \ --flattenkeywords name:_resources.* \ --outputdir results \ --name CONTRIBUTION \ robot/CONTRIBUTION_TESTS/ ``` -------------------------------- ### Extended COMPOSITION Mapping Example Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A comprehensive example of a COMPOSITION mapping including UID, facility, participation, and link details. ```json { "conformance-ehrbase.de.v0/_uid": "6e3a9506-b81c-4d74-a37f-1464fb7106b2::ehrbase.org::1", "conformance-ehrbase.de.v0/language|code": "en", "conformance-ehrbase.de.v0/language|terminology": "ISO_639-1", "conformance-ehrbase.de.v0/territory|code": "US", "conformance-ehrbase.de.v0/territory|terminology": "ISO_3166-1", "conformance-ehrbase.de.v0/category|code": "433", "conformance-ehrbase.de.v0/category|value": "event", "conformance-ehrbase.de.v0/category|terminology": "openehr", "conformance-ehrbase.de.v0/context/_health_care_facility|id": "9091", "conformance-ehrbase.de.v0/context/_health_care_facility|id_scheme": "HOSPITAL-NS", "conformance-ehrbase.de.v0/context/_health_care_facility|id_namespace": "HOSPITAL-NS", "conformance-ehrbase.de.v0/context/_health_care_facility|name": "Hospital", "conformance-ehrbase.de.v0/context/_participation:0|function": "requester", "conformance-ehrbase.de.v0/context/_participation:0|mode": "face-to-face communication", "conformance-ehrbase.de.v0/context/_participation:0|name": "Dr. Marcus Johnson", "conformance-ehrbase.de.v0/context/_participation:0|id": "199", "conformance-ehrbase.de.v0/context/_participation:0|id_scheme": "HOSPITAL-NS", "conformance-ehrbase.de.v0/context/_participation:0|id_namespace": "HOSPITAL-NS", "conformance-ehrbase.de.v0/context/start_time": "2021-12-21T14:19:31.649613+01:00", "conformance-ehrbase.de.v0/context/_end_time": "2021-12-21T15:19:31.649613+01:00", "conformance-ehrbase.de.v0/context/_location": "microbiology lab 2", "conformance-ehrbase.de.v0/context/setting|code": "238", "conformance-ehrbase.de.v0/context/setting|value": "other care", "conformance-ehrbase.de.v0/context/setting|terminology": "openehr", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|magnitude": 65.9, "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|unit": "unit", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/time": "2021-12-21T16:02:58.0094262+01:00", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/language|code": "en", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/language|terminology": "ISO_639-1", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/encoding|code": "UTF-8", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/encoding|terminology": "IANA_character-sets", "conformance-ehrbase.de.v0/_link:0|type": "problem", "conformance-ehrbase.de.v0/_link:0|meaning": "problem related note", "conformance-ehrbase.de.v0/_link:0|target": "ehr://ehr.network/347a5490-55ee-4da9-b91a-9bba710f730e", "conformance-ehrbase.de.v0/composer|name": "Silvia Blake", "conformance-ehrbase.de.v0/composer|id": "1234-5678", "conformance-ehrbase.de.v0/composer|id_scheme": "UUID", "conformance-ehrbase.de.v0/composer|id_namespace": "EHR.NETWORK" } ``` -------------------------------- ### CODE_PHRASE JSON Examples Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Examples showing the structure of CODE_PHRASE, including optional preferred term fields. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_language|code": "en", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_language|terminology": "ISO_639-1" } ``` ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_language|code": "en", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_language|terminology": "ISO_639-1", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text/_language|preferred_term": "English" } ``` -------------------------------- ### Build the project Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/ManualMappingInstruction.rst Command to clean and install the current fhir-bridge project using Maven. ```bash mvn clean install ``` -------------------------------- ### Verify Java Version Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/gettingstarted.rst Check the installed Java version to ensure compatibility. ```bash java[c] -version ``` -------------------------------- ### PARTY_IDENTIFIED Flat JSON Examples Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Examples showing minimal and full representation of PARTY_IDENTIFIED objects in flat JSON format. ```json { "conformance-ehrbase.de.v0/composer|name": "Silvia Blake" } ``` ```json { "conformance-ehrbase.de.v0/composer|name": "Silvia Blake", "conformance-ehrbase.de.v0/composer|id": "1234-5678", "conformance-ehrbase.de.v0/composer|id_scheme": "UUID", "conformance-ehrbase.de.v0/composer|id_namespace": "EHR.NETWORK", "conformance-ehrbase.de.v0/composer/_identifier:0|id": "122", "conformance-ehrbase.de.v0/composer/_identifier:0|issuer": "issuer", "conformance-ehrbase.de.v0/composer/_identifier:0|assigner": "assigner", "conformance-ehrbase.de.v0/composer/_identifier:0|type": "type" } ``` -------------------------------- ### Enable ABAC with OAuth Configuration Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/09_abac/index.rst Example environment variables to enable ABAC and configure the server URL and OAuth issuer. ```text SECURITY_AUTHTYPE=OAUTH;ABAC_DISABLED=false;ABAC_SERVER=http://localhost:3001/rest/v1/policy/execute/name/;SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_ISSUERURI=https://keycloak.PROJECT.com/auth/realms/ctr ``` -------------------------------- ### Minimal ADMIN_ENTRY JSON Example Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A basic representation of an ADMIN_ENTRY using the flat format. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/dv_text": "DV_TEXT 56", "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/language|code": "en", "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/language|terminology": "ISO_639-1", "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/encoding|code": "UTF-8", "conformance-ehrbase.de.v0/conformance_section/conformance_admin_entry/encoding|terminology": "IANA_character-sets" } ``` -------------------------------- ### Execute Composition Tests Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/02_testing/00_integration_tests.rst Examples of running composition-related tests using different tag inclusion flags. ```bash robot --include composition ``` ```bash robot -i composition ``` ```bash robot -i compositionANDjson ``` -------------------------------- ### Verify Maven Version Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/gettingstarted.rst Check the installed Maven version. ```bash mvn --version ``` -------------------------------- ### ISM_TRANSITION Full Transition Example Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Represents a complete ISM_TRANSITION including state, transition, careflow step, and reason. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/current_state|code": "532", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/current_state|value": "completed", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/current_state|terminology": "openehr", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/transition|code": "548", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/transition|value": "finish", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/transition|terminology": "openehr", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/careflow_step|code": "at0006", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/careflow_step|value": "transition", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/careflow_step|terminology": "local", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/_reason:0": "reason 1" } ``` -------------------------------- ### Run EHRbase Database with default parameters Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/04_docker_images/02_ehrbase_db/02_use_image/002_using_docker_image.rst Pulls the specified EHRbase PostgreSQL image and starts a container with default settings. ```bash docker pull ehrbase/ehrbase-postgres:11.10 docker run --name ehrdb -d -p 5432:5432 ehrbase/ehrbase-postgres:11.10 ``` -------------------------------- ### Selecting RM-Attributes Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/00_description/index.rst Example showing how to select optional Reference Model attributes using the underscore prefix. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|magnitude": 65.9, "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|unit": "unit", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_normal_range/lower|magnitude": 20.5, "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_normal_range/lower|unit": "unit", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_normal_range/upper|magnitude": 66.6, "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity/_normal_range/upper|unit": "unit" } ``` -------------------------------- ### Start EHRbase with Docker Compose Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/04_docker_images/01_ehrbase/02_use_image/002_using_docker_image.rst Commands to download the necessary configuration files and launch the containers in either foreground or detached mode. ```bash # download the docker-compose.yml file to your local wget https://github.com/ehrbase/ehrbase/raw/develop/docker-compose.yml wget https://github.com/ehrbase/ehrbase/raw/develop/.env.ehrbase docker-compose up # OR: start both containers detached, without blocking the terminal docker-compose up -d ``` -------------------------------- ### Run EHRbase Container Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/04_docker_images/01_ehrbase/01_build_image/001_build_from_dockerfile.rst Command to start a container using the default EHRbase image. ```bash docker run ehrbase/ehrbase ``` -------------------------------- ### Minimal DV_MULTIMEDIA JSON Representation Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A basic example showing the required fields for a DV_MULTIMEDIA object. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_multimedia": "http://med.tube.com/sample", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_multimedia|mediatype": "video/H261", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_multimedia|size": 504903212 } ``` -------------------------------- ### Run specific test suites with Robot Framework Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/02_testing/00_integration_tests.rst Examples of using command-line options to filter and execute specific test suites. ```bash # QUICK COPY/PASTE EXAMPLES TO RUN ONLY A SPECIFIC TEST-SUITE robot -i composition -d results --noncritical not-ready -L TRACE robot/COMPOSITION_TESTS/ robot -i contribution -d results --noncritical not-ready -L TRACE robot/CONTRIBUTION_TESTS/ robot -i directory -d results --noncritical not-ready -L TRACE robot/DIRECTORY_TESTS/ robot -i ehr_service -d results --noncritical not-ready -L TRACE robot/EHR_SERVICE_TESTS/ robot -i ehr_status -d results --noncritical not-ready -L TRACE robot/EHR_STATUS_TESTS/ robot -i knowledge -d results --noncritical not-ready -L TRACE robot/KNOWLEDGE_TESTS/ robot -i aqlANDempty_db -d results --noncritical not-ready -L TRACE robot/QUERY_SERVICE_TESTS/ robot -i aqlANDloaded_db -d results --noncritical not-ready -L TRACE robot/QUERY_SERVICE_TESTS/ ``` -------------------------------- ### Generated SDK Class Structure Source: https://github.com/ehrbase/documentation/blob/master/source/06_fhir_bridge/ManualMappingInstruction.rst Example file structure generated by the SDK for a breathing frequency composition. ```text $ opt/breathingfrequencycomposition ├── BreathrateComposition.java ├── BreathrateCompositionContainment.java ├── definition ├── RespiratoryRateObservation.java └── RespiratoryRateObservationContainment.java ``` -------------------------------- ### Web-Template Structure Example Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/00_description/index.rst A JSON representation of a Web-Template defining the tree structure and node constraints. ```json { "templateId": "conformance-ehrbase.de.v0", "semVer": "1.0.0", "version": "2.3", "defaultLanguage": "en", "languages": [ "en" ], "tree": { "id": "conformance-ehrbase.de.v0", "name": "conformance-ehrbase.de.v0", "localizedName": "conformance-ehrbase.de.v0", "rmType": "COMPOSITION", "nodeId": "openEHR-EHR-COMPOSITION.conformance_composition_.v0", "min": 1, "max": 1, "aqlPath": "", "children": [ { "id": "conformance_section", "name": "conformance section", "localizedName": "conformance section", "rmType": "SECTION", "nodeId": "openEHR-EHR-SECTION.conformance_section.v0", "min": 0, "max": 1, "aqlPath": "/content[openEHR-EHR-SECTION.conformance_section.v0]", "children": [ { "id": "conformance_observation", "name": "Conformance Observation", "localizedName": "Conformance Observation", "rmType": "OBSERVATION", "nodeId": "openEHR-EHR-OBSERVATION.conformance_observation.v0", "min": 0, "max": 1, "aqlPath": "/content[openEHR-EHR-SECTION.conformance_section.v0]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0]", "children": [ { "id": "any_event", "name": "Any event", "localizedName": "Any event", "rmType": "EVENT", "nodeId": "at0002", "min": 0, "max": -1, "aqlPath": "/content[openEHR-EHR-SECTION.conformance_section.v0]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0]/data[at0001]/events[at0002]", "children": [ { "id": "dv_quantity", "name": "DV_QUANTITY", "localizedName": "DV_QUANTITY", "rmType": "DV_QUANTITY", "nodeId": "at0008", "min": 0, "max": 1, "aqlPath": "/content[openEHR-EHR-SECTION.conformance_section.v0]/items[openEHR-EHR-OBSERVATION.conformance_observation.v0]/data[at0001]/events[at0002]/data[at0003]/items[at0008]/value", "inputs": [ { "suffix": "magnitude", "type": "DECIMAL" }, { "suffix": "unit", "type": "CODED_TEXT" } ] } ] } ] } ] } ] } } ``` -------------------------------- ### LINK Flat Data Representation Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Example of a LINK object structure in flat format. ```json { "conformance-ehrbase.de.v0/_link:0|type": "problem", "conformance-ehrbase.de.v0/_link:0|meaning": "problem related note", "conformance-ehrbase.de.v0/_link:0|target": "ehr://ehr.network/347a5490-55ee-4da9-b91a-9bba710f730e" } ``` -------------------------------- ### Flat Format Context Configuration Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/02_context/index.rst Example JSON structure defining various context fields such as language, territory, composer, and participation details. ```json { "ctx/language": "de", "ctx/territory": "US", "ctx/time": "2021-04-01T12:40:31.418954+02:00", "ctx/composer_name": "Silvia Blake", "ctx/composer_id": "123", "ctx/id_namespace": "HOSPITAL-NS", "ctx/id_scheme": "HOSPITAL-NS", "ctx/work_flow_id|id": "567", "ctx/work_flow_id|id_scheme": "HOSPITAL-NS", "ctx/work_flow_id|namespace": "HOSPITAL-NS", "ctx/work_flow_id|type": "ORGANISATION", "ctx/participation_name:0": "Dr. Marcus Johnson", "ctx/participation_function:0": "requester", "ctx/participation_mode:0": "face-to-face communication", "ctx/participation_id:0": "199", "ctx/participation_identifiers:0": "issuer1::assigner1::id1::PERSON;issuer2::assigner2::id2::PERSON", "ctx/participation_name:1": "Lara Markham", "ctx/participation_function:1": "performer", "ctx/participation_id:1": "198", "ctx/participation_identifiers:1|issuer:0": "issuer3", "ctx/participation_identifiers:1|assigner:0": "assigner3", "ctx/participation_identifiers:1|id:0": "id3", "ctx/participation_identifiers:1|type:0": "PERSON", "ctx/participation_identifiers:1|issuer:1": "issuer4", "ctx/participation_identifiers:1|assigner:1": "assigner4", "ctx/participation_identifiers:1|id:1": "id4", "ctx/participation_identifiers:1|type:1": "PERSON", "ctx/health_care_facility|name": "Hospital", "ctx/health_care_facility|id": "9091" } ``` -------------------------------- ### Simple DV_DATE JSON Representation Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A minimal JSON example representing a DV_DATE value. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_date": "2022-01-12" } ``` -------------------------------- ### Simple DV_DATE_TIME JSON Representation Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A minimal JSON example representing a DV_DATE_TIME value. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_date_time": "2022-01-12T13:22:34.000868+01:00" } ``` -------------------------------- ### Configure Composition Policy in YAML Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/09_abac/index.rst Example configuration for the composition endpoint to use a specific policy and set of parameters. ```yaml policy: composition: name: 'has_consent_template' parameters: 'organization, patient, template' ``` -------------------------------- ### ISM_TRANSITION Current State Example Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Represents the current state of an ISM_TRANSITION using a flat JSON structure. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/current_state|code": "532", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/current_state|value": "completed", "conformance-ehrbase.de.v0/conformance_section/conformance_action/ism_transition/current_state|terminology": "openehr" } ``` -------------------------------- ### Flat Format Composition Example Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/00_description/index.rst A sample JSON representation of an openEHR Composition using the Flat format. ```json { "ctx/language": "de", "ctx/territory": "US", "ctx/time": "2021-04-01T12:40:31.418954+02:00", "ctx/composer_name": "Silvia Blake", "conformance-ehrbase.de.v0/context/start_time": "2021-12-21T14:19:31.649613+01:00", "conformance-ehrbase.de.v0/context/setting|code": "238", "conformance-ehrbase.de.v0/context/setting|value": "other care", "conformance-ehrbase.de.v0/context/setting|terminology": "openehr", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|magnitude": 65.9, "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_quantity|unit": "unit" } ``` -------------------------------- ### OBJECT_REF flat representation Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Example of an OBJECT_REF structure serialized in flat JSON format. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_guideline_id|type": "GUIDELINE", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_guideline_id|namespace": "HOSPITAL-NS", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_guideline_id|id": "3445", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/_guideline_id|id_scheme": "HOSPITAL-NS" } ``` -------------------------------- ### POINT_EVENT JSON structure Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Example JSON representation for a POINT_EVENT containing text and time fields. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_text": "DV_TEXT value", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/time": "2021-12-21T16:02:58.0094262+01:00" } ``` -------------------------------- ### INSTRUCTION JSON Representation Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst Example of an INSTRUCTION object structure using flattened paths for data fields. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/current_activity/dv_text": "DV_TEXT 45", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/current_activity/timing": "R4/2022-01-31T10:00:00+01:00/P3M", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/current_activity/timing|formalism": "timing", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/dv_text": "DV_TEXT 91", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/expiry_time": "2022-01-31T10:33:28.724259+01:00", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/narrative": "Human readable instruction narrative", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/language|code": "en", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/language|terminology": "ISO_639-1", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/encoding|code": "UTF-8", "conformance-ehrbase.de.v0/conformance_section/conformance_instruction/encoding|terminology": "IANA_character-sets" } ``` -------------------------------- ### Build Documentation Source: https://github.com/ehrbase/documentation/blob/master/README.md Execute the build process for the documentation. ```bash make html ``` -------------------------------- ### Extended DV_CODED_TEXT JSON representation Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A comprehensive example including language, encoding, and mapping information. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text|value": "term1", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text|code": "at0006", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text|terminology": "local", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text|formatting": "plain", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_language|code": "en", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_language|terminology": "ISO_639-1", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_language|preferred_term": "English", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_encoding|code": "UTF-8", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_encoding|terminology": "IANA_character-sets", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_mapping:0|match": "=", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_mapping:0/target|terminology": "SNOMED-CT", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_mapping:0/target|code": "21794005", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_mapping:0/purpose|terminology": "openehr", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_mapping:0/purpose|code": "671", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text/_mapping:0/purpose|value": "research study" } ``` -------------------------------- ### Basic DV_CODED_TEXT JSON representation Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A minimal example showing the required fields for a coded text entry. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text|value": "term1", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text|code": "at0006", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/any_event:0/dv_coded_text|terminology": "local" } ``` -------------------------------- ### Comprehensive Feeder Audit Details Source: https://github.com/ehrbase/documentation/blob/master/source/08_flat/01_data_types/index.rst A full JSON example including subject, provider, location, and system audit metadata. ```json { "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/subject|id": "1234-5678", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/subject|id_scheme": "UUID", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/subject|id_namespace": "EHR.NETWORK", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/subject|name": "Silvia Blake", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/subject/_identifier:0|id": "122", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/subject/_identifier:0|issuer": "issuer", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/subject/_identifier:0|assigner": "assigner", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/subject/_identifier:0|type": "type", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/provider|id": "1234-5678", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/provider|id_scheme": "UUID", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/provider|id_namespace": "EHR.NETWORK", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/provider|name": "Silvia Blake", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/provider/_identifier:0|id": "122", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/provider/_identifier:0|issuer": "issuer", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/provider/_identifier:0|assigner": "assigner", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/provider/_identifier:0|type": "type", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/location|id": "12342341", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/location|id_scheme": "NMC", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/location|id_namespace": "uk.org.nmc", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit/location|name": "Org 1", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit|system_id": "orig", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit|version_id": "final", "conformance-ehrbase.de.v0/conformance_section/conformance_observation/_feeder_audit/feeder_system_audit|time": "2021-12-21T16:02:58.0094262+01:00" } ``` -------------------------------- ### Enable management endpoints via command line Source: https://github.com/ehrbase/documentation/blob/master/source/03_development/08_status_and_metrics/usage/index.rst Set the environment variable before starting the JAR file to enable the management environment endpoint. ```bash $~/ehrbase: export MANAGEMENT_ENDPOINT_ENV_ENABLE=true $~/ehrbase: java -jar application/target/application-0.15.0.jar ```