Merge

.github/workflows/config-preprocessor-build.yml

@@ -0,0 +1,49 @@
+name: config-processor-build
+
+on:
+  push:
+
+env:
+  DOCKER_IMAGE_NAME: ghcr.io/loculus-project/config-processor
+
+defaults:
+  run:
+    working-directory: ./kubernetes/config-processor
+
+concurrency:
+  group: ci-${{ github.ref }}-config-processor
+  cancel-in-progress: true
+
+jobs:
+  dockerImage:
+    name: Build config-processor Docker Image
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      checks: read
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Docker metadata
+        id: dockerMetadata
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }}
+            type=sha,prefix=commit-
+      - name: Build and push image
+        uses: docker/build-push-action@v5
+        with:
+          context: ./kubernetes/config-processor
+          push: true
+          tags: ${{ steps.dockerMetadata.outputs.tags }}

.github/workflows/node_dev.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v4
     - name: Install yaml package
-      run: pip install PyYAML
+      run: pip install PyYAML requests
 
     - name: Generate local test config
       run: ./generate_local_test_config.sh

.gitignore

@@ -16,3 +16,5 @@ node_modules/
 # logs
 /log
 
+temp/
+

README.md

@@ -45,7 +45,7 @@ export DOCKER_DEFAULT_PLATFORM=linux/amd64
 
 ### User management
 
-We use keycloak for authorization. The keycloak instance is deployed in the `loculus` namespace and exposed to the outside either under `localhost:8083` or `authentication.[your-argo-cd-path]`. The keycloak instance is configured with a realm called `loculusRealm` and a client called `test-cli`. The realm is configured to use the exposed url of keycloak as a [frontend url](https://www.keycloak.org/server/hostname).
+We use keycloak for authorization. The keycloak instance is deployed in the `loculus` namespace and exposed to the outside either under `localhost:8083` or `authentication-[your-argo-cd-path]`. The keycloak instance is configured with a realm called `loculusRealm` and a client called `test-cli`. The realm is configured to use the exposed url of keycloak as a [frontend url](https://www.keycloak.org/server/hostname).
 For testing we added multiple users to the realm. The users are:
 - `admin` with password `admin` (login under `your-exposed-keycloak-url/admin/master/console/`)
 - `testuser` with password `testuser` (login under `your-exposed-keycloak-url/realms/loculusRealm/account/`)
@@ -56,7 +56,7 @@ For testing we added multiple users to the realm. The users are:
 ### Group management
 
  - Groups are entities managed by the backend, uniquely identified by a name.
- - Every sequence entry is owned by the group that it was initially submitted for. Modifications (edits while staging, revisions, revocations) can only be made by members of that group.
+ - Every sequence entry is owned by the group that it was initially submitted for. Modifications (edits while awaiting approval, revisions, revocations) can only be made by members of that group.
  - Each user can be a member of multiple groups.
  - Users can create new groups, becoming the initial member automatically.
  - Group members have the authority to add or remove other members.

backend/README.md

@@ -32,7 +32,7 @@ You need to set:
 ```
 * the path to the config file (use `../generate_local_test_config.sh` to generate this file):
 ```
---backend.config.path=../website/tests/config/backend_config.json
+--loculus.config.path=../website/tests/config/backend_config.json
 ```
 * the url to fetch the public key for JWT verification 
   (corresponding to the `jwks_uri` value in the `/.well-known/openid-configuration` endpoint of the Keycloak server):

backend/docs/plantuml/sequenceRevocation.puml

@@ -6,7 +6,7 @@
     frontend -> backend: wants to revoke already processed sequence
 
      alt accession exists and highest version is 'APPROVED_FOR_RELEASE'
-        backend -> DB: insert new version\nwith status 'REVISION_STAGING' \nand ' is_revocation = true'
+        backend -> DB: insert new version\nwith status 'AWAITING_APPROVAL_FOR_REVOCATION' \nand ' is_revocation = true'
     backend -> frontend: response with accession + new version number
     else
         backend -> frontend: response with error message