Release/v5.0.0

CHANGELOG.md

@@ -17,6 +17,33 @@ Please refer to the respective repositories for a more in depth changelog of sin
 |TORCH|<https://github.com/medizininformatik-initiative/torch|
 |Blaze FHIR server|<https://github.com/samply/blaze>|
 
+
+## [5.0.0] - 2024-11-21
+
+### Ontology
+
+This Release is based on ontology Version [v3.0.0](https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/tag/v3.0.0)
+
+
+### Overall
+
+- Updated all components to new versions
+- Made FLARE execute-cohort endpoint only available on local docker network and new FLARE version makes enabling execute-cohort endpoint configurable
+- Added Fhir-Data-Evaluator (FDE) to triangle
+
+### Features
+
+| Feature | Affected Components |
+| -- | -- |
+|UI Re-Design, Restructuring of Code|UI, Backend|
+|Extended Criteria Search (Elastic Search)|UI, Backend, Ontology Generation|
+|Add OAuth2 to triangle components|TORCH, FLARE|
+|Added Dataselection and Extraction |UI, Backend, Ontology Generation, TORCH|
+|Migrated from Mapping code system tree strcture to poly tree structure to support non strict hierarchical code systems like sct |UI, Backend, Ontology Generation, TORCH, FLARE|
+|Loading and displaying of criteria availability |UI, Backend, Ontology Generation|
+|Added new modules and Updated Ontology|UI, Backend, Ontology Generation, FLARE, sq2cq, TORCH|
+
+
 ## [5.0.0-alpha.1] - 2024-11-15
 
 ### Overall

feasibility-portal/backend/.env.default

@@ -54,7 +54,6 @@ DATAPORTAL_BACKEND_QUERYRESULT_EXPIRY_MINUTES=5
 DATAPORTAL_BACKEND_LOG_LEVEL_SQL=info
 DATAPORTAL_BACKEND_LOG_LEVEL=info
 # ---- Elastic Search
-DATAPORTAL_BACKEND_ELASTIC_SEARCH_ENABLED=true
 DATAPORTAL_BACKEND_ELASTIC_SEARCH_HOST=dataportal-elastic
 DATAPORTAL_BACKEND_ELASTIC_SEARCH_FILTER=context,terminology,kds_module
 DATAPORTAL_ES_INIT_EXIT_ON_EXISTING_INDICES=false

feasibility-portal/backend/docker-compose.yml

@@ -1,7 +1,7 @@
 services:
   dataportal-backend:
     restart: unless-stopped
-    image: ghcr.io/medizininformatik-initiative/feasibility-backend:6.0.0-alpha.6
+    image: ghcr.io/medizininformatik-initiative/feasibility-backend:6.0.0
     ports:
     - ${DATAPORTAL_BACKEND_PORT:-127.0.0.1:8091}:8090
     depends_on:
@@ -82,7 +82,6 @@ services:
       PRIVACY_THRESHOLD_SITES_RESULT: ${DATAPORTAL_BACKEND_PRIVACY_THRESHOLD_SITES_RESULT:-0}
       QUERYRESULT_DISABLE_LOG_FILE_ENCRYPTION: "true"
       # ---- Elastic Search
-      ELASTIC_SEARCH_ENABLED: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_ENABLED:-true}
       ELASTIC_SEARCH_HOST: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_HOST:-dataportal-elastic}
       ELASTIC_SEARCH_FILTER: ${DATAPORTAL_BACKEND_ELASTIC_SEARCH_FILTER:-context,terminology,kds_module}
       # ---- logging

feasibility-portal/gui/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   dataportal-ui:
-    image: ghcr.io/medizininformatik-initiative/feasibility-gui:6.0.0-alpha.6
+    image: ghcr.io/medizininformatik-initiative/feasibility-gui:6.0.1
     restart: unless-stopped
     volumes:
       - ./deploy-config.json:/usr/share/nginx/html/assets/config/config.deploy.json

feasibility-portal/keycloak/docker-compose.yml

@@ -1,7 +1,7 @@
 
 services:
   auth-db:
-    image: postgres:15-alpine
+    image: postgres:17-alpine
     restart: unless-stopped
     environment:
       POSTGRES_DB: ${FEASIBILITY_KC_DB:-keycloakdb}
@@ -11,7 +11,7 @@ services:
       - "feasibility-auth-db:/var/lib/postgresql/data"
 
   auth:
-    image: keycloak/keycloak:25.0
+    image: keycloak/keycloak:26.0
     command: ["start", "--import-realm"]
     restart: unless-stopped
     environment:

feasibility-triangle/.gitignore

@@ -2,3 +2,5 @@
 /testdata/*.json
 /testdata/*.zip
 troubleshooting/input-queries.json
+fhir-data-evaluator/output/*
+!fhir-data-evaluator/output/README.md

feasibility-triangle/fhir-data-evaluator/.env.default

@@ -0,0 +1,21 @@
+FDE_CONVERT_TO_CSV=false
+FDE_FHIR_SERVER=http://localhost:8080/fhir
+FDE_FHIR_USER=
+FDE_FHIR_PASSWORD=
+FDE_FHIR_MAX_CONNECTIONS=4
+FDE_FHIR_MAX_QUEUE_SIZE=500
+FDE_FHIR_PAGE_COUNT=1000
+FDE_FHIR_BEARER_TOKEN=
+FDE_FHIR_OAUTH_ISSUER_URI=
+FDE_FHIR_OAUTH_CLIENT_ID=
+FDE_FHIR_OAUTH_CLIENT_SECRET=
+FDE_MAX_IN_MEMORY_SIZE_MIB=10
+FDE_INPUT_MEASURE=./measure/kds-measure.json
+FDE_OUTPUT_DIR=./output
+FDE_TZ=Europe/Berlin
+FDE_FHIR_REPORT_DESTINATION_SERVER=http://localhost:8080/fhir
+FDE_SEND_REPORT_TO_SERVER=true
+FDE_AUTHOR_IDENTIFIER_SYSTEM=http://dsf.dev/sid/organization-identifier
+FDE_AUTHOR_IDENTIFIER_VALUE=fde-dic
+FDE_PROJECT_IDENTIFIER_SYSTEM=http://medizininformatik-initiative.de/sid/project-identifier
+FDE_PROJECT_IDENTIFIER_VALUE=fdpg-data-availability-report

feasibility-triangle/fhir-data-evaluator/README.md

@@ -0,0 +1,41 @@
+# The Fhir-Data-Evaluator (FDE)
+
+The FDE is used as part of the feasibility triangle to collect metadata about available data on the local FHIR server.
+This data can then be sent via the DSF to the central portal or loaded into the local portal to display the availability of single criteria in the fhir server.
+
+## Running the FDE
+
+To run the FDE copy the .env.default file to .env in the this folder and change the env variables according to your requirements.
+
+Run the FDE by executing the `run-fde` script provided here.
+
+You can as is configured by default send the metadata report back to your FHIR server which contains your patient data or
+alternatively send the data to a different fhir server.
+
+Regardless of this choice, the FHIR server which contains the report should be accessible from your DSE BPE in order to send the report to the central fdpg DSF using the
+data transfer plugin https://github.com/medizininformatik-initiative/mii-process-data-transfer.
+
+
+| Env Variable                                    | Description                                                                                          | Default                                       | Possible Values                                 |
+|-------------------------------------------------|------------------------------------------------------------------------------------------------------|-----------------------------------------------|-------------------------------------------------|
+| FDE_CONVERT_TO_CSV                              | Whether to convert the data to CSV format                                                            | false                                         | true, false                                     |
+| FDE_FHIR_SERVER                                 | Base URL of the FHIR server                                                                          | http://localhost:8080/fhir                    | URL                                             |
+| FDE_FHIR_USER                                   | Username for the FHIR server authentication                                                          | (empty)                                       | String                                          |
+| FDE_FHIR_PASSWORD                               | Password for the FHIR server authentication                                                          | (empty)                                       | String                                          |
+| FDE_FHIR_MAX_CONNECTIONS                        | Maximum number of simultaneous connections to the FHIR server                                        | 4                                             | Integer                                         |
+| FDE_FHIR_MAX_QUEUE_SIZE                         | Maximum size of the FHIR server request queue                                                        | 500                                           | Integer                                         |
+| FDE_FHIR_PAGE_COUNT                             | Number of resources to fetch per page                                                                | 1000                                          | Integer                                         |
+| FDE_FHIR_BEARER_TOKEN                           | Bearer token for FHIR server authentication                                                          | (empty)                                       | String                                          |
+| FDE_FHIR_OAUTH_ISSUER_URI                       | OAuth issuer URI for FHIR server                                                                     | (empty)                                       | URL                                             |
+| FDE_FHIR_OAUTH_CLIENT_ID                        | OAuth client ID for FHIR server                                                                      | (empty)                                       | String                                          |
+| FDE_FHIR_OAUTH_CLIENT_SECRET                    | OAuth client secret for FHIR server                                                                  | (empty)                                       | String                                          |
+| FDE_MAX_IN_MEMORY_SIZE_MIB                      | Maximum size (in MiB) of in-memory data storage                                                      | 10                                            | Integer                                         |
+| FDE_INPUT_MEASURE                               | Path to the input measure JSON file                                                                  | ./measure/kds-measure.json                    | File path                                       |
+| FDE_OUTPUT_DIR                                  | Directory to save output files                                                                       | ./output                                      | Directory path                                  |
+| FDE_TZ                                          | Time zone to use for processing                                                                      | Europe/Berlin                                 | Time zone                                       |
+| FDE_FHIR_REPORT_DESTINATION_SERVER              | FHIR server to send reports to                                                                       | http://localhost:8080/fhir                    | URL                                             |
+| FDE_SEND_REPORT_TO_SERVER                       | Whether to send the generated report to the server                                                   | true                                          | true, false                                     |
+| FDE_AUTHOR_IDENTIFIER_SYSTEM                    | System for the author's identifier                                                                   | http://dsf.dev/sid/organization-identifier    | URL                                             |
+| FDE_AUTHOR_IDENTIFIER_VALUE                     | Value for the author's identifier                                                                    | fde-dic                                       | String                                          |
+| FDE_PROJECT_IDENTIFIER_SYSTEM                   | System for the project's identifier                                                                  | http://medizininformatik-initiative.de/sid/project-identifier | URL                             |
+| FDE_PROJECT_IDENTIFIER_VALUE                    | Value for the project's identifier                                                                   | fdpg-data-availability-report                 | String                                          |

feasibility-triangle/fhir-data-evaluator/docker-compose.yml

@@ -0,0 +1,30 @@
+services:
+  fhir-data-evaluator:
+    image: ghcr.io/medizininformatik-initiative/fhir-data-evaluator:pr-48
+    environment:
+      CONVERT_TO_CSV: ${FDE_CONVERT_TO_CSV:-true}
+      FHIR_SERVER: ${FDE_FHIR_SERVER:-http://localhost:8080/fhir}
+      FHIR_USER: ${FDE_FHIR_USER:-}
+      FHIR_PASSWORD: ${FDE_FHIR_PASSWORD:-}
+      FHIR_MAX_CONNECTIONS: ${FDE_FHIR_MAX_CONNECTIONS:-4}
+      FHIR_MAX_QUEUE_SIZE: ${FDE_FHIR_MAX_QUEUE_SIZE:-500}
+      FHIR_PAGE_COUNT: ${FDE_FHIR_PAGE_COUNT:-1000}
+      FHIR_BEARER_TOKEN: ${FDE_FHIR_BEARER_TOKEN:-}
+      FHIR_OAUTH_ISSUER_URI: ${FDE_FHIR_OAUTH_ISSUER_URI:-}
+      FHIR_OAUTH_CLIENT_ID: ${FDE_FHIR_OAUTH_CLIENT_ID:-}
+      FHIR_OAUTH_CLIENT_SECRET: ${FDE_FHIR_OAUTH_CLIENT_SECRET:-}
+      MAX_IN_MEMORY_SIZE_MIB: ${FDE_MAX_IN_MEMORY_SIZE_MIB:-10}
+      SEND_REPORT_TO_SERVER: ${FDE_SEND_REPORT_TO_SERVER:-false}
+      AUTHOR_IDENTIFIER_SYSTEM: ${FDE_AUTHOR_IDENTIFIER_SYSTEM:-http://dsf.dev/sid/organization-identifier}
+      AUTHOR_IDENTIFIER_VALUE: ${FDE_AUTHOR_IDENTIFIER_VALUE:-fde-dic}
+      PROJECT_IDENTIFIER_SYSTEM: ${FDE_PROJECT_IDENTIFIER_SYSTEM:-http://medizininformatik-initiative.de/sid/project-identifier}
+      PROJECT_IDENTIFIER_VALUE: ${FDE_PROJECT_IDENTIFIER_VALUE:-fdpg-data-availability-report}
+      FHIR_REPORT_DESTINATION_SERVER: ${FDE_FHIR_REPORT_DESTINATION_SERVER:-http://localhost:8080/fhir}
+      TZ: ${FDE_TZ:-Europe/Berlin}
+    extra_hosts:
+      - "auth.localhost:host-gateway"
+      - "localhost:host-gateway"
+    volumes:
+    - "${FDE_INPUT_MEASURE:-./measure/kds-measure.json}:/app/measure.json"
+    - "${FDE_OUTPUT_DIR:-./output}:/app/output"
+    - ../auth:/app/certs