Merge pull request #100 from medizininformatik-initiative/release/v5.…

…0.0-alpha.1 Release/v5.0.0 alpha.1
medizininformatik-initiative · Nov 15, 2024 · 411bb71 · 411bb71
2 parents b2d271b + 33220b1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,14 +17,21 @@ 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-alpha.1] - 2024-11-15
+
+### 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
+
 
 ## [5.0.0-alpha] - 2024-10-21
 
 ### Features
 
 | Feature | Affected Components |
 | -- | -- |
-|UI Re-Desig, Restructuring of Code|UI, Backend|
+|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|

diff --git a/feasibility-portal/backend/.env.default b/feasibility-portal/backend/.env.default
@@ -53,5 +53,9 @@ DATAPORTAL_BACKEND_QUERYRESULT_EXPIRY_MINUTES=5
 # ---- logging
 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
 
diff --git a/feasibility-portal/backend/docker-compose.yml b/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.3
+    image: ghcr.io/medizininformatik-initiative/feasibility-backend:6.0.0-alpha.6
     ports:
     - ${DATAPORTAL_BACKEND_PORT:-127.0.0.1:8091}:8090
     depends_on:
@@ -108,7 +108,7 @@ services:
         source: dataportal-postgres-data
         target: /var/lib/postgresql/data
   dataportal-elastic:
-    image: docker.elastic.co/elasticsearch/elasticsearch:8.15.0
+    image: docker.elastic.co/elasticsearch/elasticsearch:8.16.0
     ports:
       - "127.0.0.1:9200:9200"
       - "127.0.0.1:9300:9300"
@@ -128,22 +128,18 @@ services:
         source: dataportal-elastic-data
         target: /usr/share/elasticsearch/data
   init-elasticsearch:
-    image: curlimages/curl:8.8.0
+    image: ghcr.io/medizininformatik-initiative/dataportal-es-init:latest
     depends_on:
       dataportal-elastic:
         condition: service_healthy
     environment:
-      ELASTIC_HOST: http://dataportal-elastic:9200
-      ELASTIC_GIT_TAG: v3.0.0-test.2
-      ELASTIC_FILEPATH: https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/TAGPLACEHOLDER/example/fdpg-ontology/
-      ELASTIC_FILENAME: elastic.zip
-      # if set to false, existing indices are not overridden.
-      OVERRIDE_EXISTING: true
-    entrypoint: [ "sh", "-c", "/tmp/init.sh" ]
-    volumes:
-      - type: bind
-        source: ./elastic-init.sh
-        target: /tmp/init.sh
+      ES_HOST: http://dataportal-elastic
+      ES_PORT: 9200
+      ONTO_GIT_TAG: v3.0.0-alpha.1
+      ONTO_REPO: https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/
+      ONTO_RELATIVE_PATH: /example/fdpg-ontology/
+      DOWNLOAD_FILENAME: elastic.zip
+      EXIT_ON_EXISTING_INDICES: ${DATAPORTAL_ES_INIT_EXIT_ON_EXISTING_INDICES:-false}
 
 volumes:
   dataportal-postgres-data:

diff --git a/feasibility-portal/gui/docker-compose.yml b/feasibility-portal/gui/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   dataportal-ui:
-    image: ghcr.io/medizininformatik-initiative/feasibility-gui:6.0.0-alpha.4
+    image: ghcr.io/medizininformatik-initiative/feasibility-gui:6.0.0-alpha.6
     restart: unless-stopped
     volumes:
       - ./deploy-config.json:/usr/share/nginx/html/assets/config/config.deploy.json
diff --git a/feasibility-triangle/fhir-server/docker-compose.yml b/feasibility-triangle/fhir-server/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   fhir-server:
-    image: samply/blaze:0.28
+    image: samply/blaze:0.30
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: 5s
@@ -30,7 +30,7 @@ services:
     - "${FHIR_SERVER_OPENID_CLIENT_TRUST_STORE:-../auth/trust-store.p12}:/app/trust-store.p12"
 
   fhir-server-frontend:
-    image: samply/blaze-frontend:0.27.1
+    image: samply/blaze-frontend:0.30
     healthcheck:
       test: ["CMD-SHELL", "wget --spider http://127.0.0.1:3000/fhir/"]
       interval: 5s

diff --git a/feasibility-triangle/flare/.env.default b/feasibility-triangle/flare/.env.default
@@ -16,3 +16,4 @@ FLARE_LOG_LEVEL=info
 FLARE_FHIR_OAUTH_ISSUER_URI=https://example.org:444/auth/realms/blaze
 FLARE_FHIR_OAUTH_CLIENT_ID=account
 FLARE_FHIR_OAUTH_CLIENT_SECRET=insecure
+FLARE_ENABLE_COHORT_ENDPOINT=false
diff --git a/feasibility-triangle/flare/docker-compose.yml b/feasibility-triangle/flare/docker-compose.yml
@@ -1,10 +1,11 @@
 services:
   flare:
-    image: ghcr.io/medizininformatik-initiative/flare:2.4.0-alpha.2
+    image: ghcr.io/medizininformatik-initiative/flare:2.4.0-alpha.3
     ports:
       - ${FEASIBILITY_FLARE_PORT:-127.0.0.1:8084}:8080
     environment:
       FLARE_FHIR_SERVER: ${FLARE_FHIR_SERVER_URL:-http://fhir-server:8080/fhir/}
+      FLARE_ENABLE_COHORT_ENDPOINT: ${FLARE_ENABLE_COHORT_ENDPOINT:-false}
       FLARE_FHIR_USER: ${FLARE_FHIR_USER:-}
       FLARE_FHIR_PASSWORD: ${FLARE_FHIR_PW:-}
       FLARE_FHIR_MAX_CONNECTIONS: ${FLARE_FHIR_MAX_CONNECTIONS:-32}

diff --git a/feasibility-triangle/rev-proxy/conf.d/flare.conf.template b/feasibility-triangle/rev-proxy/conf.d/flare.conf.template
@@ -17,4 +17,8 @@ server {
         proxy_pass http://$upstream$request_uri;
         proxy_set_header Authorization "";
     }
+
+    location /query/execute-cohort {
+        auth_basic "Restricted";
+    }
 }
diff --git a/feasibility-triangle/rev-proxy/conf.d/torch.conf.template b/feasibility-triangle/rev-proxy/conf.d/torch.conf.template
@@ -23,7 +23,7 @@ server {
         auth_basic_user_file /etc/nginx/.htpasswd;
         set $upstream torch-nginx:8080;
         rewrite ^/fileserver/(.*)$ /$1 break;
-        proxy_pass http://torch-nginx:8080;
+        proxy_pass http://$upstream;
         proxy_set_header Authorization "";
     }
 }
diff --git a/feasibility-triangle/rev-proxy/context-paths.nginx.conf b/feasibility-triangle/rev-proxy/context-paths.nginx.conf
@@ -135,6 +135,10 @@ http {
             proxy_set_header     Authorization "";
         }
 
+        location /query/execute-cohort {
+            auth_basic           "Restricted";
+        }
+
 
     }
 }
diff --git a/feasibility-triangle/torch/docker-compose.yml b/feasibility-triangle/torch/docker-compose.yml
@@ -9,7 +9,7 @@ services:
         - triangle-torch-data-store:/app/output
   torch:
     restart: unless-stopped
-    image: ghcr.io/medizininformatik-initiative/torch:1.0.0-alpha.1
+    image: ghcr.io/medizininformatik-initiative/torch:1.0.0-alpha.3
     ports:
       - ${TORCH_PORT:-127.0.0.1:8086}:8080
     environment: