better-care · Sep 3, 2024 · Sep 3, 2024 · Sep 4, 2024 · Sep 9, 2024 · Sep 10, 2024
diff --git a/README.md b/README.md
@@ -1,3 +1,306 @@
+# AQL BUILDER WRITTEN BY BETTER AND ADAPTED BY SASURFER (@GITHUB)
+_WARNING: for EHRBase versions < 2.5.0 use release 1.0.0. Use latest version for EHRBase version >= 2.14.0 . No version available for 2.5.0<= EHRBase version<2.14.0__
+
+ This sofware helps in building openEHR aql queries. It needs a running instance of EHRBase in order to work. Its main capabilities are: creating the query with autocompletion and template visualization, saving queries on the running instance of EHRBase (called views) or locally (called snippets), performing queries, retrieving and showing the results, importing (writing into EHRBase) templates. More info at [aql builder site]( https://docs.better.care/studio/aql-builder/overview ).
+
+At login are asked: Username, Password, Platform URL. If oauth2 is configured (see below on how to do it) then the client_secret is also requested. The platform URL has the form http://{yourehrbaseservername}:{yourehrbaseserverport}/ehrbase
+
+NOTE: It is necessary to login with the EHRBase admin credentials to let all template and views methods work as intended.
+
+Example of values for the default credentials:
+- Username: ehrbase-admin
+- Password: EvenMoreSecretPassword
+- Platform URL: http://localhost:8080/ehrbase
+
+
+## INSTALL LOCALLY 
+Conda is optional. You can install with or without it.
+
+Clone the repository:
+```
+git clone https://github.com/sasurfer/aqlbetter.git
+```
+creates, optionally, a conda environment and install nodejs and run install and build scripts:
+```
+cd aqlbetter
+conda create --name aqlbetter
+conda activate aqlbetter
+conda install -c conda-forge nodejs
+npm install -g @angular/cli@10.1.0
+cd projects/aql-builder/
+npm install --save-dev @angular-devkit/build-angular --force
+export NODE_OPTIONS=--openssl-legacy-provider
+ng build aql-builder --prod
+```
+
+## COMMON CONFIGURATION
+Modify 'localhost:8080' in projects/aql-builder/src/proxy.conf.json with {youehrbaseservername}:{yourehrbaseserverport}. 
+This step, though optional, ensures that the app uses the EHRBase nodename, e.g., local.ehrbase.org, to create the full name for the queries. If the server in proxy is not recognized a default nodename will be used instead. 
+
+## RUN WITH BASIC AUTH
+
+### EHRBASE CONFIGURATION
+In the EHRBase directory creates two files: .env.ehrbase and docker-compose.yml
+
+This is an example of .env.ehrbase (read by docker-compose.yaml):
+```
+SERVER_NODENAME=local.ehrbase.org
+SECURITY_AUTHTYPE=BASIC
+SECURITY_AUTHUSER=ehrbase-user
+SECURITY_AUTHPASSWORD=SuperSecretPassword
+SECURITY_AUTHADMINUSER=ehrbase-admin
+SECURITY_AUTHADMINPASSWORD=EvenMoreSecretPassword
+SECURITY_OAUTH2USERROLE=USER
+SECURITY_OAUTH2ADMINROLE=ADMIN
+SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_ISSUERURI=
+MANAGEMENT_ENDPOINTS_WEB_EXPOSURE=env,health,info,metrics,prometheus
+MANAGEMENT_ENDPOINTS_WEB_BASEPATH=/management
+MANAGEMENT_ENDPOINT_ENV_ENABLED=true
+MANAGEMENT_ENDPOINT_HEALTH_ENABLED=true
+MANAGEMENT_ENDPOINT_HEALTH_DATASOURCE_ENABLED=true
+MANAGEMENT_ENDPOINT_INFO_ENABLED=true
+MANAGEMENT_ENDPOINT_METRICS_ENABLED=true
+MANAGEMENT_ENDPOINT_PROMETHEUS_ENABLED=FALSE
+MANAGEMENT_ENDPOINT_HEALTH_PROBES_ENABLED=true
+MANAGEMENT_ENDPOINT_ENV_SHOWVALUES=ALWAYS
+SYSTEM_ALLOW_TEMPLATE_OVERWRITE=true
+EHRBASE_TEMPLATE_ALLOW_OVERWRITE=true
+ADMIN_API_ACTIVE=true
+CACHE_ENABLED=true
+ADMINAPI_ALLOWDELETEALL=true
+WEB_CORS_ALLOWEDORIGINS=http://localhost:4201
+WEB_CORS_ALLOWEDORIGINPATTERNS=http://*.localhost:4201
+WEB_CORS_ALLOWEDMETHODS=GET,PUT,DELETE,POST,OPTIONS,HEAD
+WEB_CORS_ALLOWCREDENTIALS=true
+WEB_CORS_ALLOWEDHEADERS=*
+```
+and the related docker-compose.yml:
+```
+version: '3'
+
+#
+# Minimal setup for a running EHRbase. Contains the server component as well as the required postgres instance.
+#
+services:
+
+  #
+  # EHRBase container. see `.env.ehrbase` for configuration details.
+  #
+  ehrbase:
+    image: ${EHRBASE_IMAGE:-ehrbase/ehrbase:2.15.0}
+    env_file:
+      - .env.ehrbase
+    environment:
+      DB_URL: jdbc:postgresql://ehrdb:5432/ehrbase
+      DB_USER_ADMIN: ehrbase
+      DB_PASS_ADMIN: ehrbase
+      DB_USER: ehrbase_restricted
+      DB_PASS: ehrbase_restricted
+    links:
+      - ehrdb
+    depends_on:
+      ehrdb:
+        condition: service_healthy
+    ports:
+      - "8080:8080"
+    networks:
+      - ehrbase-net
+
+  #
+  # Pre-configured ehrbase postgres.
+  #
+  ehrdb:
+    image: ${EHRBASE_POSTGRES_IMAGE:-ehrbase/ehrbase-v2-postgres:16.2}
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      EHRBASE_USER_ADMIN: ehrbase
+      EHRBASE_PASSWORD_ADMIN: ehrbase
+      EHRBASE_USER: ehrbase_restricted
+      EHRBASE_PASSWORD: ehrbase_restricted
+    healthcheck:
+      test: [ "CMD-SHELL", "pg_isready -U postgres" ]
+      interval: 5s
+      timeout: 5s
+      retries: 12
+    ports:
+      - "5432:5432"
+    networks:
+      - ehrbase-net
+    volumes:
+      - ./.pgdata:/var/lib/postgresql/data      
+networks:
+  ehrbase-net: { }
+```
+Start the services:
+```
+docker compose up 
+```
+### AQLBETTER CONFIGURATION
+Make sure to use {aqlbetter_dir}/projects/aql-builder/src/environments/environment.prod.ts.BASICAUTH
+From the dir {aqlbetter_dir}/projects/aql-builder:
+```
+cp ./src/environments/environment.prod.ts.BASICAUTH ./src/environments/environment.prod.ts
+
+```
+Remember to rerun the build step:
+```
+ng build aql-builder --prod
+```
+### RUN
+Run with:
+```
+ng serve aql-builder --port 4201
+```
+Open a browser tab to localhost:4201, fill the credentials and click "Start querying data".
+
+## OAUTH2
+### EHRBASE CONFIGURATION
+Create a directory for EHRBase and copy the following two example files.
+
+This is an example of .env.ehrbase (read by docker compose yaml):
+```
+SERVER_NODENAME=local.ehrbase.org
+SECURITY_AUTHTYPE=OAUTH
+SECURITY_AUTHUSER=ehrbase-user
+SECURITY_AUTHPASSWORD=SuperSecretPassword
+SECURITY_AUTHADMINUSER=ehrbase-admin
+SECURITY_AUTHADMINPASSWORD=EvenMoreSecretPassword
+SECURITY_OAUTH2USERROLE=USER
+SECURITY_OAUTH2ADMINROLE=ADMIN
+SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_ISSUERURI=http://172.31.0.2:8080/auth/realms/ehrbase
+MANAGEMENT_ENDPOINTS_WEB_EXPOSURE=env,health,info,metrics,prometheus
+MANAGEMENT_ENDPOINTS_WEB_BASEPATH=/management
+MANAGEMENT_ENDPOINT_ENV_ENABLED=true
+MANAGEMENT_ENDPOINT_HEALTH_ENABLED=true
+MANAGEMENT_ENDPOINT_HEALTH_DATASOURCE_ENABLED=true
+MANAGEMENT_ENDPOINT_INFO_ENABLED=true
+MANAGEMENT_ENDPOINT_METRICS_ENABLED=true
+MANAGEMENT_ENDPOINT_PROMETHEUS_ENABLED=FALSE
+MANAGEMENT_ENDPOINT_HEALTH_PROBES_ENABLED=true
+MANAGEMENT_ENDPOINT_ENV_SHOWVALUES=ALWAYS
+SYSTEM_ALLOW_TEMPLATE_OVERWRITE=true
+ADMIN_API_ACTIVE=true
+CACHE_ENABLED=true
+ADMINAPI_ALLOWDELETEALL=true
+WEB_CORS_ALLOWEDORIGINS=http://localhost:4201
+WEB_CORS_ALLOWEDORIGINPATTERNS=http://*.localhost:4201
+WEB_CORS_ALLOWEDMETHODS=GET,PUT,DELETE,POST,OPTIONS,HEAD
+WEB_CORS_ALLOWCREDENTIALS=true
+WEB_CORS_ALLOWEDHEADERS=*
+```
+and the docker-compose.yml:
+```
+version: '3'
+
+#
+# Minimal setup for a running EHRbase. Contains the server component as well as the required postgres instance.
+#
+services:
+
+  #
+  # EHRBase container. see `.env.ehrbase` for configuration details.
+  #
+  ehrbase:
+    image: ${EHRBASE_IMAGE:-ehrbase/ehrbase:2.6.0}
+    env_file:
+      - .env.ehrbase
+    environment:
+      DB_URL: jdbc:postgresql://ehrdb:5432/ehrbase
+      DB_USER_ADMIN: ehrbase
+      DB_PASS_ADMIN: ehrbase
+      DB_USER: ehrbase_restricted
+      DB_PASS: ehrbase_restricted
+    links:
+      - ehrdb
+      - keycloak3
+    depends_on:
+      ehrdb:
+        condition: service_healthy
+      keycloak3:
+        condition: service_started
+    ports:
+      - "8080:8080"
+    networks:
+      - ehrbase-net
+
+  #
+  # Pre-configured ehrbase postgres.
+  #
+  ehrdb:
+    image: ${EHRBASE_POSTGRES_IMAGE:-ehrbase/ehrbase-v2-postgres:16.2}
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      EHRBASE_USER_ADMIN: ehrbase
+      EHRBASE_PASSWORD_ADMIN: ehrbase
+      EHRBASE_USER: ehrbase_restricted
+      EHRBASE_PASSWORD: ehrbase_restricted
+    healthcheck:
+      test: [ "CMD-SHELL", "pg_isready -U postgres" ]
+      interval: 5s
+      timeout: 5s
+      retries: 12
+    ports:
+      - "5432:5432"
+    networks:
+      - ehrbase-net
+    volumes:
+      - ./.pgdata:/var/lib/postgresql/data      
+
+  keycloak3:
+    image: quay.io/keycloak/keycloak:24.0.3
+    #image: registry.vitasystems.dev/docker-registry/keycloak-x:0.9.9
+    container_name: keycloak3
+    command: "start-dev --import-realm"
+    ports:
+      - "8081:8080"
+    environment:
+      KEYCLOAK_ADMIN: admin
+      KEYCLOAK_ADMIN_PASSWORD: admin
+      KC_HTTP_RELATIVE_PATH: /auth
+      KC_HTTP_PORT: 8080
+    volumes:
+      - ./tests/keycloak/import:/opt/keycloak/data/import
+    networks:
+      - ehrbase-net
+
+networks:
+  ehrbase-net: { }
+```
+from the latest https://github.com/ehrbase/ehrbase.git copy the path to the file (included) tests/keycloak/import/ehrbase-realm-exported.json to this directory.
+
+Modify the SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_ISSUERURI server and port with your keycloak ip and port.
+
+Start the services:
+```
+docker compose up 
+```
+
+### AQLBETTER CONFIGURATION
+Use {aqlbetter_dir}/projects/aql-builder/src/environments/environment.prod.ts.OAUTH2 and modify the authorizationUrl according to your installation of keycloak. Remember that the address (server:port) must be the same as the one given in SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_ISSUERURI in the EHRBase settings (172.31.0.2:8080 in the example).
+Rerun the build step:
+```
+ng build aql-builder --prod
+```
+### KEYCLOAK
+Open a browser tab to localhost:8081/auth/admin and login to keycloak (admin/admin). Create, inside the ehrbase realm, a client named aqlbetter with client_id=aqlbetter, the urls set to http://localhost:4201 and Authentication and OAuth 2.0 Device Authorization Grant flagged on, choose client_id and client_secret as credentials and copy the newly created client_secret. Reset the ehrbase-admin password and copy it. client_secret and password for ehrbase-admin will be needed for the login form. 
+
+### RUN
+Run with:
+```
+ng serve aql-builder --port 4201 --prod
+```
+Open a browser tab to localhost:4201, fill the credentials and click "Start querying data".
+
+## Acknowledgments
+This work has been partially funded by the following sources:
+<li>“Total Patient Management” (ToPMa) project (grant by the Sardinian Regional Authority, grant number RC_CRP_077);</li>
+<li>the “Processing, Analysis, Exploration, and Sharing of Big and/or Complex Data” (XDATA) project (grant by the Sardinian Regional Authority). 
+</li><ul>
+
+# ORIGINAL README FROM BETTER FOLLOWS
+
 # Better UI components
 
 ![Lint all packages](https://github.com/better-care/better-ui-components/workflows/Lint%20all%20packages/badge.svg)

diff --git a/angular.json b/angular.json
@@ -274,7 +274,8 @@
         "serve": {
           "builder": "@angular-devkit/build-angular:dev-server",
           "options": {
-            "browserTarget": "aql-builder:build"
+            "browserTarget": "aql-builder:build",
+	    "proxyConfig": "projects/aql-builder/src/proxy.conf.json"
           },
           "configurations": {
             "production": {