rename to loculus (#713)

remove extraneous comment

rename files

missed this file

restore org name to pathoplexus

.github/scripts/collect_kubernetes_logs.sh

@@ -2,13 +2,13 @@
 
 set -e
 
-pods=$(kubectl get pods -l app=pathoplexus -n pathoplexus -o jsonpath='{.items[*].metadata.name}' || true)
+pods=$(kubectl get pods -l app=loculus -n loculus -o jsonpath='{.items[*].metadata.name}' || true)
 for pod in $pods; do
-  containers=$(kubectl get pod "$pod" -n pathoplexus -o jsonpath='{.spec.containers[*].name}' || true)
+  containers=$(kubectl get pod "$pod" -n loculus -o jsonpath='{.spec.containers[*].name}' || true)
   for container in $containers; do
     mkdir "kubernetes_logs" -p
     file="kubernetes_logs/$pod-$container.txt"
     echo "Logs from $pod - $container:" >> "$file"
-    kubectl logs "$pod" -n pathoplexus -c "$container" >> "$file" 2>/dev/null || true
+    kubectl logs "$pod" -n loculus -c "$container" >> "$file" 2>/dev/null || true
   done
 done

.github/scripts/wait_for_pods_to_be_ready.py

@@ -27,7 +27,7 @@ def main():
 
 
 def get_pods():
-    cmd = ['kubectl', 'get', 'pods', '-l', 'app=pathoplexus', '-n', 'pathoplexus', '-o', 'json']
+    cmd = ['kubectl', 'get', 'pods', '-l', 'app=loculus', '-n', 'loculus', '-o', 'json']
     result = subprocess.run(cmd, capture_output=True, text=True)
     return json.loads(result.stdout)['items']
 

.github/workflows/e2e-k3d.yml

@@ -109,10 +109,10 @@ jobs:
       run: kubectl get pods --all-namespaces
     - name: Describe pods
       if: ${{ !cancelled() }}
-      run: kubectl describe pods -l app=pathoplexus -n pathoplexus
+      run: kubectl describe pods -l app=loculus -n loculus
     - name: Show events
       if: ${{ !cancelled() }}
-      run: kubectl get events -n pathoplexus
+      run: kubectl get events -n loculus
 
     - name: Save logs from all containers to file
       if: ${{ !cancelled() }}

.github/workflows/update-argocd-metadata.yml

@@ -40,8 +40,8 @@ jobs:
     - name: Checkout External Repository
       uses: actions/checkout@v4
       with:
-        repository: 'pathoplexus/argocd_metadata' # Replace with the correct repository path
-        token: ${{ secrets.ARGOCD_METADATA_PAT }} # Personal Access Token with appropriate permissions
+        repository: 'loculus/argocd_metadata'
+        token: ${{ secrets.ARGOCD_METADATA_PAT }}
 
     - name: Modify config.json
       run: |
@@ -53,8 +53,8 @@ jobs:
 
     - name: Commit and Push Changes
       run: |
-        git config --global user.name 'Pathoplexus bot'
-        git config --global user.email 'bot@pathoplexus.org'
+        git config --global user.name 'Loculus bot'
+        git config --global user.email 'bot@loculus.org'
         git add config.json
         git commit -m "Update config.json"
         git push

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# Contributing to Pathoplexus
+# Contributing to Loculus
 
 Contributions are very welcome! Just fork the repository, develop in a branch and submit a pull request.
 
@@ -17,7 +17,7 @@ We value clean code, here are some guidelines on what we consider clean code:
   Every piece of the code should at least be tested in the happy path.
 * Develop code with testability in mind.
 
-Keep in mind that Pathoplexus is designed to be run and maintained by anyone. 
+Keep in mind that Loculus is designed to be run and maintained by anyone. 
 This means that the code that we develop needs to be suitably general and configurable.
 
 ### OpenAPI docs

README.md

@@ -1,4 +1,4 @@
-# pathoplexus
+# loculus
 
 Detailed documentation is available in each folder's README. This file contains a high-level overview of the project and shared documentation that is best kept in one place.
 
@@ -38,15 +38,15 @@ export DOCKER_DEFAULT_PLATFORM=linux/amd64
 ```
 
 ## Authorization
-We use keycloak for authorization. The keycloak instance is deployed in the `pathoplexus` 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 `pathoplexusRealm` 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/pathoplexusRealm/account/`)
+- `testuser` with password `testuser` (login under `your-exposed-keycloak-url/realms/loculusRealm/account/`)
 - and more testusers, for each browser in the e2e test following the pattern: `testuser_[processId]_[browser]` with password `testuser_[processId]_[browser]` 
 - These testusers will be added to the `testGroup` in the setup for e2e tests. If you change the number of browsers in the e2e test, you need to adapt `website/tests/playwrightSetup.ts` accordingly. 
 
-## Contributing to Pathoplexus
+## Contributing to Loculus
 
 Contributions are very welcome!
-Please see [`CONTRIBUTING.md`](https://github.com/pathoplexus/pathoplexus/blob/main/CONTRIBUTING.md)
+Please see [`CONTRIBUTING.md`](https://github.com/pathoplexus/loculus/blob/main/CONTRIBUTING.md)
 for more information or ping us in case you need help.

backend/README.md

@@ -1,4 +1,4 @@
-# Pathoplexus Backend
+# Loculus Backend
 
 ## Setup
 
@@ -15,7 +15,7 @@ All commands mentioned in this section are run from the `backend` directory unle
 
 ```bash
 ../generate_local_test_config.sh
-./gradlew bootRun --args='--spring.datasource.url=jdbc:postgresql://localhost:5432/pathoplexus --spring.datasource.username=postgres --spring.datasource.password=unsecure --backend.config.path=../website/tests/config/backend_config.json --spring.security.oauth2.resourceserver.jwt.jwk-set-uri=http://localhost:8083/realms/pathoplexusRealm/protocol/openid-connect/certs'
+./gradlew bootRun --args='--spring.datasource.url=jdbc:postgresql://localhost:5432/loculus --spring.datasource.username=postgres --spring.datasource.password=unsecure --backend.config.path=../website/tests/config/backend_config.json --spring.security.oauth2.resourceserver.jwt.jwk-set-uri=http://localhost:8083/realms/loculusRealm/protocol/openid-connect/certs'
 ```
 
 #### Details
@@ -26,7 +26,7 @@ that need to be passed on startup, e.g. via command line argument.
 You need to set:
 * the database URL, username and password:
 ```
---spring.datasource.url=jdbc:postgresql://localhost:5432/pathoplexus
+--spring.datasource.url=jdbc:postgresql://localhost:5432/loculus
 --spring.datasource.username=postgres
 --spring.datasource.password=unsecure
 ```
@@ -37,7 +37,7 @@ You need to set:
 * 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):
 ```
---spring.security.oauth2.resourceserver.jwt.jwk-set-uri=http://localhost:8083/realms/pathoplexusRealm/protocol/openid-connect/certs
+--spring.security.oauth2.resourceserver.jwt.jwk-set-uri=http://localhost:8083/realms/loculusRealm/protocol/openid-connect/certs
 ```
 
 We use Flyway, so that the service can provision an empty/existing DB without any manual steps in between. On startup scripts in `src/main/resources/db/migration` are executed in order, i.e. `V1__*.sql` before `V2__*.sql` if they didn't run before, so that the DB is always up-to-date. (For more info on the naming convention, see [this](https://www.red-gate.com/blog/database-devops/flyway-naming-patterns-matter) blog post.)

backend/build.gradle

@@ -10,7 +10,7 @@ plugins {
     id 'org.springdoc.openapi-gradle-plugin' version '1.8.0'
 }
 
-group = 'org.pathoplexus'
+group = 'org.loculus'
 version = '0.0.1'
 
 java {

backend/docs/plantuml/sequenceInitialSubmission.puml

@@ -1,7 +1,7 @@
 @startuml
-    participant "Pathoplexus Frontend / User" as frontend #LightCyan
+    participant "Loculus Frontend / User" as frontend #LightCyan
     participant "(Pre-)Processing Pipeline" as processing #LightGreen
-    participant "Pathoplexus Backend" as backend #Orange
+    participant "Loculus Backend" as backend #Orange
     database "Database" as DB
 
     frontend -> backend: submit initial sequence data

backend/docs/plantuml/sequenceRevision.puml

@@ -1,6 +1,6 @@
 @startuml
-    participant "Pathoplexus Frontend / User" as frontend #LightCyan
-    participant "Pathoplexus Backend" as backend #Orange
+    participant "Loculus Frontend / User" as frontend #LightCyan
+    participant "Loculus Backend" as backend #Orange
     database "Database" as DB