Merge pull request #45 from medizininformatik-initiative/release/v3.1.0

Release/v3.1.0
medizininformatik-initiative · Nov 9, 2023 · f5121cb · f5121cb
2 parents c9ca6af + aa3657f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,13 +9,35 @@ Please refer to the respective repositories for a more in depth changelog of sin
 |Component|Link|
 |--|--|
 |UI|<https://github.com/medizininformatik-initiative/feasibility-gui>|
+|Ontology Generation|<https://github.com/medizininformatik-initiative/fhir-ontology-generator>|
 |Backend|<https://github.com/medizininformatik-initiative/feasibility-backend>|
 |AKTIN Broker|<https://github.com/aktin/broker>|
 |AKTIN Feasibility Plugin|<https://github.com/medizininformatik-initiative/feasibility-aktin-plugin>|
 |DSF Feasibility Plugin|<https://github.com/medizininformatik-initiative/feasibility-dsf-process>|
 |FLARE|<https://github.com/medizininformatik-initiative/flare>|
 |Blaze FHIR server|<https://github.com/medizininformatik-initiative/blaze>|
 
+## [3.0.0] - 2023-08-08
+
+### Overall
+
+- Updated all components and underlying libraries to the new versions
+- Updated all components to version compatible with ontology version 2.0
+- Adjusted readme to reflect changes in the underlying components
+
+### Features
+
+| Feature | Affected Components |
+| -- | -- |
+|Added support for referenced criteria|UI, backend, Ontology, Sq2cql, FLARE|
+|Added support for composite search parameters|UI, SQ, Ontology, Sq2cql, FLARE|
+|Updated to new DSF version v1.0.0 compatible with new DSF verison v1.x | Backend, DSF feasibility plugin|
+|Added Dateselection|UI|
+|Update ontology to new ontology generation and added ontology to images directly| Ontology, Backend, FLARE|
+|Added encrypted result logging| Backend|
+|Add support for self-signed certificates| Backend, FLARE, DSF feasibility plugin |
+
+
 ## [2.1.0] - 2023-07-25
 
 ### Overall

diff --git a/feasibility-portal/README.md b/feasibility-portal/README.md
@@ -17,7 +17,7 @@ ssh to your virtual machine and switch to sudo `sudo -s`.
 Designate a folder for your setup in which you clone the deploy repository, we suggest /opt (`cd /opt`)
 Navigate to the directory and clone this repository: `git clone https://github.com/medizininformatik-initiative/feasibility-deploy.git`
 Navigate to the feasibility-portal folder of the repository: `cd /opt/feasibility-deploy/feasibility-portal`
-Checkout the version (git tag) of the feasibility portal you would like to install: `git checkout tags/<your-tag-name-here>`
+Checkout the version (git tag) of the feasibility portal you would like to install: `git checkout <your-tag-name-here>`
 
 ### Step 3 - Initialise .env files
 
@@ -35,27 +35,9 @@ Set the rights for all files of the auth folder to 655 `chmod 655 /opt/feasibili
 
 - Not providing the certificate files is not an option.
 
-### Step 5 - Load the ontology mapping files
+### Step 5 - Load the ontology
 
-If used, (see "Overview") The FLARE component requires a mapping file and ontology tree file to translate an incoming feasibility query into FHIR Search queries.
-Both can be downloaded here: https://confluence.imi.med.fau.de/display/ABIDEMI/Ontologie
-
-Upload the ontology .zip files to your server, unpack them and copy the ontology files to your feasibility portal ontology folder
-
-```bash
-sudo -s
-mkdir /<path>/<to>/<folder>/<of>/<choice>
-cd /<path>/<to>/<folder>/<of>/<choice>
-unzip mapping_*.zip
-unzip ui_profile_*.zip
-unzip db_migration_*.zip
-cd mapping
-cp * /opt/feasibility-deploy/feasibility-portal/ontology
-cd ../ui_profile
-cp * /opt/feasibility-deploy/feasibility-portal/ontology/ui_profiles
-cd ../db_migration
-cp * /opt/feasibility-deploy/feasibility-portal/ontology/migration
-```
+**Note:** The ontology is now part of the image and will not have to be loaded manually.
 
 ### Step 6 - Configure your feasibility portal
 
@@ -73,7 +55,7 @@ If you use the default local feasibility portal setup you will only have to chan
 | backend/.env           | FLARE_WEBSERVICE_BASE_URL                  | http://flare:8080                                                  |
 | backend/.env           | FEASIBILITY_BACKEND_ALLOWED_ORIGINS        | base-url-of-your-local-feasibility-portal                          |
 |backend/.env            |FEASIBILITY_BACKEND_KEYCLOAK_BASE_URL_ISSUER| base-url-of-your-local-feasibility-portal/auth                     |
-| gui/deploy-config.json | uiBackendApi > baseUrl                     | base-url-of-your-local-feasibility-portal/api/v2                   |
+| gui/deploy-config.json | uiBackendApi > baseUrl                     | base-url-of-your-local-feasibility-portal/api/v3                   |
 | gui/deploy-config.json | auth > baseUrl                             | base-url-of-your-local-feasibility-portal                          |
 
 Please note that all user env variables (variables containing USER) should be changed and all password variables (variables containing PASSWORD or PW) should be set to secure passwords.
@@ -129,7 +111,46 @@ Click on **New query**, create a query and send it using the **send** button.
 After a few moments you should see the results to your query in the **Number of patients** window.
 
 
-## Configurable environment variables
+## Updating your local feasibility portal
+
+If you have already installed the local feasibility portal and just want to update it, follow these steps:
+
+
+### Step 1 - Stop your portal
+
+`cd /opt/feasibility-deploy/feasibility-portal && bash stop-feasibility-portal.sh`
+
+### Step 2 - Update repository and check out new tag
+
+`cd /opt/feasibility-deploy && git pull`
+`git checkout <new-tag>`
+
+### Step 3 - transfer the new env variables
+
+Compare the .env and .env.default files for each component and add any new variables from the .env.default file to the .env file.
+Keep the existing configuration as is.
+
+### Step 4 - Update your ontology
+
+**Note:** The ontology is now part of the image and will not have to be loaded manually.
+
+### Step 5 - Start your portal
+
+To start the portal navigate to `/opt/feasibility-deploy/feasibility-portal` and
+execute `bash start-feasibility-portal-local.sh`.
+
+### Step 6 - Log in to the local feasibility portal and test your connection
+
+Ask for the Url of the central portal at the FDPG or check Confluence for the correct address.
+
+Log in to the portal and send a request with the Inclusion Criterion chosen from the Inclusion criteria tree (folder sign under Inclusion Criteria) 
+"Person > PatientIn > Geschlecht: Female,Male"
+
+and press "send".
+
+## Configuration
+
+### Configurable environment variables
 
 
 | Env Var                                                                           | Description                                                                                                                                                                  | Default                                            | Possible values | Component |
@@ -210,60 +231,15 @@ After a few moments you should see the results to your query in the **Number of
 | FEASIBILITY_DSF_BROKER_PROCESS_FHIR_SERVER_BASE_URL                               | Base URL to a FHIR server or proxy for feasibility evaluation. This can also be the base URL of a reverse proxy if used. Only required if evaluation strategy is set to cql. | https://dsf-zars-fhir-proxy/fhir                   | URL             | DSF       |
 
 
+### Support for self-signed certificates
 
-## Updating your local feasibility portal
-
-If you have already installed the local feasibility portal and just want to update it, follow these steps:
-
-
-### Step 1 - Stop your portal
-
-`cd /opt/feasibility-deploy/feasibility-portal && bash stop-feasibility-portal.sh`
-
-### Step 2 - Update repository and check out new tag
-
-`cd /opt/feasibility-deploy && git pull`
-`git checkout <new-tag>`
-
-### Step 3 - transfer the new env variables
-
-Compare the .env and .env.default files for each component and add any new variables from the .env.default file to the .env file.
-Keep the existing configuration as is.
-
-### Step 4 - Update your ontology
-
-If used, (see "Overview") The FLARE component requires a mapping file and ontology tree file to translate an incoming feasibility query into FHIR Search queries.
-Both can be downloaded here: https://confluence.imi.med.fau.de/display/ABIDEMI/Ontologie
-
-Upload the ontology .zip files to your server, unpack them and copy the ontology files to your feasibility portal ontology folder.
-
-```bash
-sudo -s
-mkdir /<path>/<to>/<folder>/<of>/<choice>
-cd /<path>/<to>/<folder>/<of>/<choice>
-unzip mapping_*.zip
-unzip ui_profile_*.zip
-unzip db_migration_*.zip
-cd mapping
-cp * /opt/feasibility-deploy/feasibility-portal/ontology
-cd ../ui_profile
-cp * /opt/feasibility-deploy/feasibility-portal/ontology/ui_profiles
-cd ../db_migration
-cp * /opt/feasibility-deploy/feasibility-portal/ontology/migration
-```
-
-Existing files should be replaced.
-
-### Step 5 - Start your portal
+Depending on your setup you might need to use self-singed certificates and the tools will have to accept your CAs.
+For the portal then only tool for which this is relevant is the backend.
 
-To start the portal navigate to `/opt/feasibility-deploy/feasibility-portal` and
-execute `bash start-feasibility-portal-local.sh`.
+#### Feasibility Backend
 
-### Step 6 - Log in to the local feasibility portal and test your connection
+The feasibility backend supports the use of self-signed certificates from your own CAs. On each startup, the feasibility backend will search through the folder /app/certs inside the container, add all found CA *.pem files to a java truststore and start the application with this truststore.
 
-Ask for the Url of the central portal at the FDPG or check Confluence for the correct address.
+Using docker-compose, mount a folder from your host (e.g.: ./certs) to the /app/certs folder, add your *.pem files (one for each CA you would like to support) to the folder and ensure that they have the .pem extension.
 
-Log in to the portal and send a request with the Inclusion Criterion chosen from the Inclusion criteria tree (folder sign under Inclusion Criteria) 
-"Person > PatientIn > Geschlecht: Female,Male"
-
-and press "send".
+In this deployment repository we have prepared this for you. To add your own CA add the respective ca *.pem files to the backend/certs folder.
diff --git a/feasibility-portal/backend/.env.default b/feasibility-portal/backend/.env.default
@@ -3,6 +3,8 @@ FEASIBILITY_BACKEND_CQL_TRANSLATE_ENABLED=true
 FEASIBILITY_BACKEND_FHIR_TRANSLATE_ENABLED=false
 FEASIBILITY_BACKEND_API_BASE_URL=https://localhost/api/
 FEASIBILITY_BACKEND_ALLOWED_ORIGINS=https://localhost
+FEASIBILITY_BACKEND_ONTOLOGY_ORDER="Diagnose, Prozedur, Person, Laboruntersuchung, Medikamentenverabreichung, Bioprobe, Einwilligung"
+FEASIBILITY_BACKEND_MAX_SAVED_QUERIES_PER_USER=100
 # ---- db config
 FEASIBILITY_BACKEND_DATASOURCE_HOST=feasibility-gui-backend-db
 FEASIBILITY_BACKEND_DATASOURCE_PORT=5432

diff --git a/feasibility-portal/backend/docker-compose.yml b/feasibility-portal/backend/docker-compose.yml
@@ -1,7 +1,7 @@
 version: '3.7'
 services:
   feasibility-gui-backend:
-    image: ghcr.io/medizininformatik-initiative/feasibility-backend:3.0.0
+    image: ghcr.io/medizininformatik-initiative/feasibility-backend:4.1.0
     ports:
     - ${FEASIBILITY_BACKEND_PORT:-127.0.0.1:8091}:8090
     depends_on:
@@ -14,6 +14,8 @@ services:
       API_BASE_URL: ${FEASIBILITY_BACKEND_API_BASE_URL:-https://localhost/api/}
       ALLOWED_ORIGINS: ${FEASIBILITY_BACKEND_ALLOWED_ORIGINS:-https://localhost}
       QUERYRESULT_EXPIRY_MINUTES: ${FEASIBILITY_BACKEND_QUERYRESULT_EXPIRY_MINUTES:-5}
+      ONTOLOGY_ORDER: ${FEASIBILITY_BACKEND_ONTOLOGY_ORDER:-"Diagnose, Prozedur, Person, Laboruntersuchung, Medikamentenverabreichung, Bioprobe, Einwilligung"}
+      MAX_SAVED_QUERIES_PER_USER: ${FEASIBILITY_BACKEND_MAX_SAVED_QUERIES_PER_USER:-100}
       # ---- db config
       FEASIBILITY_DATABASE_HOST: ${FEASIBILITY_BACKEND_DATASOURCE_HOST:-feasibility-gui-backend-db}
       FEASIBILITY_DATABASE_PORT: ${FEASIBILITY_BACKEND_DATASOURCE_PORT:-5432}
@@ -59,16 +61,14 @@ services:
       PRIVACY_QUOTA_READ_DETAILED_OBFUSCATED_INTERVALSECONDS: ${FEASIBILITY_BACKEND_PRIVACY_QUOTA_READ_DETAILED_OBFUSCATED_INTERVALSECONDS:-7200}
       PRIVACY_THRESHOLD_RESULTS: ${FEASIBILITY_BACKEND_PRIVACY_THRESHOLD_RESULTS:-20}
       PRIVACY_THRESHOLD_SITES: ${FEASIBILITY_BACKEND_PRIVACY_THRESHOLD_SITES:-3}
+      QUERYRESULT_DISABLE_LOG_FILE_ENCRYPTION: "true"
       # ---- logging
       LOG_LEVEL_SQL: ${FEASIBILITY_BACKEND_LOG_LEVEL_SQL:-warn}
       LOG_LEVEL: ${FEASIBILITY_BACKEND_LOG_LEVEL:-warn}
     restart: unless-stopped
     volumes:
-      - ${FEASIBILITY_BACKEND_UI_PROFILES_PATH:-../ontology/ui_profiles}:/opt/codex-feasibility-backend/ontology/ui_profiles
-      - ${FEASIBILITY_BACKEND_CONCEPT_TREE_PATH:-../ontology/codex-code-tree.json}:/opt/codex-feasibility-backend/ontology/codex-code-tree.json
-      - ${FEASIBILITY_BACKEND_TERM_CODE_MAPPING_PATH:-../ontology/codex-term-code-mapping.json}:/opt/codex-feasibility-backend/ontology/codex-term-code-mapping.json
-      - ${FEASIBILITY_BACKEND_MIGRATION_PATH:-../ontology/migration/R__Load_latest_ui_profile.sql}:/opt/codex-feasibility-backend/ontology/migration/R__Load_latest_ui_profile.sql
       - ${FEASIBILITY_BACKEND_CERTS_PATH:-../secrets}:/opt/codex-feasibility-security
+      - ./certs:/opt/codex-feasibility-backend/certs
 
   feasibility-gui-backend-db:
     image: 'postgres:15-alpine'
@@ -79,3 +79,11 @@ services:
       POSTGRES_PASSWORD: ${FEASIBILITY_BACKEND_DATASOURCE_PASSWORD:-guidbpw}
       POSTGRES_DB: codex_ui
     restart: unless-stopped
+    volumes:
+    - type: volume
+      source: feas-backend-db-data
+      target: /var/lib/postgresql/data
+
+volumes:
+  feas-backend-db-data:
+    name: "feas-backend-db-data"
diff --git a/feasibility-portal/gui/deploy-config.json.default b/feasibility-portal/gui/deploy-config.json.default
@@ -6,7 +6,7 @@
     "baseUrl": "/api"
   },
   "uiBackendApi": {
-    "baseUrl": "https://localhost/api/v2"
+    "baseUrl": "https://localhost/api/v3"
   },
   "auth": {
     "baseUrl": "https://localhost/auth",
@@ -28,10 +28,14 @@
     "extra": {
       "displayvaluefiltericon": false,
       "showoptionspage": true,
-      "optionpageroles": ["FeasibilityAdmin"]
+      "showdataselectionpage": false,
+      "optionpageroles": ["FeasibilityAdmin"],
+      "displayInfoMessage": true,
+      "displayUpdateInfo": false
     }
   },
   "options": {
+    "sendsqcontexttobackend": true,
     "pollingtimeinseconds": 30,
     "pollingintervallinseconds": 10,
     "lowerboundarypatientresult": 0,
@@ -46,5 +50,6 @@
   "stylesheet": "FDPGTheme",
   "fhirport": "8082",
   "dataset": "codex",
-  "queryVersion": "v2"
+  "queryVersion": "v2",
+  "proposalPortalLink": "https://antrag.dev.forschen-fuer-gesundheit.de"
 }
diff --git a/feasibility-portal/gui/docker-compose.yml b/feasibility-portal/gui/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   feasibility-gui:
-    image: ghcr.io/medizininformatik-initiative/feasibility-gui:1.0.0
+    image: ghcr.io/medizininformatik-initiative/feasibility-gui:2.1.0
     ports:
     - "443:8443"
     restart: unless-stopped