Merge pull request #354 from medizininformatik-initiative/release/v6.…

…0.0-alpha.1 Release v6.0.0 alpha.1
medizininformatik-initiative · Sep 2, 2024 · cf5b856 · cf5b856
2 parents c460f75 + b182c16
commit cf5b856
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diff --git a/.github/integration-test/docker-compose.yml b/.github/integration-test/docker-compose.yml
@@ -16,6 +16,7 @@ services:
       API_BASE_URL: "http://localhost:8091/api/"
       ALLOWED_ORIGINS: "https://localhost"
       QUERYRESULT_EXPIRY_MINUTES: 5
+      ELASTIC_SEARCH_ENABLED: "false"
       # ---- db config
       FEASIBILITY_DATABASE_HOST: "feasibility-gui-backend-db"
       FEASIBILITY_DATABASE_PORT: 5432
@@ -66,6 +67,8 @@ services:
       - ./ontology/ui_profiles:/opt/codex-feasibility-backend/ontology/ui_profiles
       - ./ontology/codex-code-tree.json:/opt/codex-feasibility-backend/ontology/codex-code-tree.json
       - ./ontology/codex-term-code-mapping.json:/opt/codex-feasibility-backend/ontology/codex-term-code-mapping.json
+      - ./ontology/terminology_systems.json:/opt/codex-feasibility-backend/ontology/terminology_systems.json
+      - ./ontology/dse/profile_tree.json:/opt/codex-feasibility-backend/ontology/dse/profile_tree.json
       - ./ontology/migration/R__Load_latest_ui_profile.sql:/opt/codex-feasibility-backend/ontology/migration/R__Load_latest_ui_profile.sql
       - ./secrets:/opt/codex-feasibility-security
   feasibility-gui-backend-db:

diff --git a/.github/integration-test/ontology/dse/profile_tree.json b/.github/integration-test/ontology/dse/profile_tree.json
@@ -0,0 +1,63 @@
+{
+    "name": "Root",
+    "module": "no-module",
+    "url": "no-url",
+    "children": [
+        {
+            "id": "de5c2903-00aa-4d64-92e5-2161d56e3daf",
+            "children": [
+                {
+                    "id": "69f4718f-1767-4517-90f8-6c079f627eed",
+                    "name": "MII_PR_Medikation_MedicationStatement",
+                    "display": "MII PR Medikation MedicationStatement",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement",
+                    "leaf": true,
+                    "selectable": true
+                },
+                {
+                    "id": "83b4d6be-b3e1-451a-adf2-c307477e7b97",
+                    "name": "MII_PR_Medikation_Medikationsliste",
+                    "display": "MII PR Medikation Medikationsliste",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/medikationsliste",
+                    "leaf": true,
+                    "selectable": true
+                },
+                {
+                    "id": "fd375ed9-b3cd-414f-8a56-c70e10bb9609",
+                    "name": "MII_PR_Medikation_MedicationRequest",
+                    "display": "MII PR Medikation MedicationRequest",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationRequest",
+                    "leaf": true,
+                    "selectable": true
+                },
+                {
+                    "id": "323a3ad1-1c10-45f5-848a-2dc5fb100c47",
+                    "name": "MII_PR_Medikation_Medication",
+                    "display": "MII PR Medikation Medication",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/Medication",
+                    "leaf": true,
+                    "selectable": true
+                },
+                {
+                    "id": "81ed0f03-1d77-49c9-8391-d4c25702652c",
+                    "name": "MII_PR_Medikation_MedicationAdministration",
+                    "display": "MII PR Medikation MedicationAdministration",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationAdministration",
+                    "leaf": true,
+                    "selectable": true
+                }
+            ],
+            "name": "modul-medikation",
+            "display": "Medikation",
+            "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement",
+            "module": "modul-medikation",
+            "selectable": true,
+            "leaf": false
+        }
+    ]
+}
diff --git a/.github/integration-test/ontology/terminology_systems.json b/.github/integration-test/ontology/terminology_systems.json
@@ -0,0 +1,18 @@
+[
+  {
+    "url": "http://loinc.org",
+    "name": "loinc"
+  },
+  {
+    "url": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
+    "name": "ICD-10"
+  },
+  {
+    "url": "http://fhir.de/CodeSystem/bfarm/ops",
+    "name": "OPS"
+  },
+  {
+    "url": "TBD",
+    "name": "obviously this is just an example"
+  }
+]
diff --git a/.github/scripts/create-keycloak-user.sh b/.github/scripts/create-keycloak-user.sh
@@ -1,6 +1,6 @@
 #!/bin/bash -e
 
-docker exec -u0 integration-test_auth_1 /opt/keycloak/bin/kcadm.sh config credentials --server http://localhost:8080/auth --realm master --user keycloakadmin --password keycloak
-docker exec -u0 integration-test_auth_1 /opt/keycloak/bin/kcadm.sh create users -s username=testuser -s email=test@example.com -s enabled=true -s emailVerified=true -r feasibility
-docker exec -u0 integration-test_auth_1 /opt/keycloak/bin/kcadm.sh add-roles --uusername testuser --rolename FeasibilityUser -r feasibility
-docker exec -u0 integration-test_auth_1 /opt/keycloak/bin/kcadm.sh set-password -r feasibility --username testuser --new-password testpassword
+docker exec -u0 integration-test-auth-1 /opt/keycloak/bin/kcadm.sh config credentials --server http://localhost:8080/auth --realm master --user keycloakadmin --password keycloak
+docker exec -u0 integration-test-auth-1 /opt/keycloak/bin/kcadm.sh create users -s username=testuser -s email=test@example.com -s enabled=true -s emailVerified=true -r feasibility
+docker exec -u0 integration-test-auth-1 /opt/keycloak/bin/kcadm.sh add-roles --uusername testuser --rolename FeasibilityUser -r feasibility
+docker exec -u0 integration-test-auth-1 /opt/keycloak/bin/kcadm.sh set-password -r feasibility --username testuser --new-password testpassword
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -145,7 +145,7 @@ jobs:
         run: .github/scripts/download-and-unpack-ontology.sh
 
       - name: Run Feasibility Backend with Database, Keycloak and Blaze
-        run: docker-compose -f .github/integration-test/docker-compose.yml up -d
+        run: docker compose -f .github/integration-test/docker-compose.yml up -d
 
       - name: Wait for Feasibility Backend
         run: .github/scripts/wait-for-url.sh  http://localhost:8091/actuator/health

diff --git a/.gitignore b/.gitignore
@@ -50,7 +50,10 @@ googleCodeStyle.xml
 /ontology/mapping_cql.json
 /ontology/mapping_fhir.json
 /ontology/mapping_tree.json
-
+/ontology/dse
+/ontology/terminology-systems.json
 /logging/
 
 result.log
+ontology
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,7 +4,18 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
-## [5.0.A] - 2024-06-29
+## [6.0.0-alpha.1] - 2024-09-02
+
+### Added
+- Terminology search implemented via external elastic search service ([#307](https://github.com/medizininformatik-initiative/feasibility-backend/issues/307))
+- Endpoints to query profile data for data selection and extraction (ES) ([#321](https://github.com/medizininformatik-initiative/feasibility-backend/issues/321))
+- Endpoints to search for codeable concepts (ES) ([#324](https://github.com/medizininformatik-initiative/feasibility-backend/issues/324))
+### Changed
+- **breaking** Consistent naming for endpoints and filenames (kebab-case for rest endpoints, camelCase for json parameters, snake_case for elastic search variables)
+### Security
+- Updated Spring Boot to 3.3.2 ([#317](https://github.com/medizininformatik-initiative/feasibility-backend/issues/317))
+
+## [5.0.1] - 2024-06-29
 
 ### Fixed
 - Injection of environment variable value for OAuth client id was broken ([#308](https://github.com/medizininformatik-initiative/feasibility-backend/issues/308))
@@ -19,7 +30,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Updated sq2cql to v0.3.0
 - Updated ontology to version v2.2.0 ([#299](https://github.com/medizininformatik-initiative/feasibility-backend/issues/299))
 ### Fixed
-- Increased timeout in MockBrockerClientIT to avoid occasional test failures ([#276](https://github.com/medizininformatik-initiative/feasibility-backend/issues/276))
+- Increased timeout in MockBrokerClientIT to avoid occasional test failures ([#276](https://github.com/medizininformatik-initiative/feasibility-backend/issues/276))
 - OPS codes with lowercase letters are now correctly found ([#292](https://github.com/medizininformatik-initiative/feasibility-backend/issues/292))
 ### Security
 - updated spring boot to 3.3.1

diff --git a/Dockerfile b/Dockerfile
@@ -7,7 +7,7 @@ WORKDIR /opt/codex-feasibility-backend
 COPY ./target/*.jar ./feasibility-gui-backend.jar
 COPY ontology ontology
 
-RUN addgroup --system feasibility && adduser --system feasibility --ingroup feasibility
+RUN groupadd --system feasibility && useradd --system feasibility -g feasibility
 RUN mkdir logging
 RUN chown -R feasibility:feasibility /opt/codex-feasibility-backend