feat: Edit group info

README.md

@@ -31,9 +31,9 @@ Additional documentation for development is available in each folder's README. T
 
 If you would like to develop with a full local loculus instance for development you need to:
 
-1. Deploy a local kubernetes instance: [kubernetes](/kubernetes/README.md)
-2. Deploy the backend: [backend](/backend/README.md)
-3. Deploy the frontend/website: [website](/website/README.md)
+1. Deploy a local kubernetes instance: [kubernetes](./kubernetes/README.md)
+2. Deploy the backend: [backend](./backend/README.md)
+3. Deploy the frontend/website: [website](./website/README.md)
 
 Note that if you are developing the backend or frontend/website in isolation a full local loculus instance is not required. See the individual READMEs for more information.
 
@@ -79,6 +79,7 @@ For testing we added multiple users to the realm. The users are:
 - Each user can be a member of multiple submitting groups.
 - Users can create new submitting groups, becoming the initial member automatically.
 - Group members have the authority to add or remove other members.
+- Group members have the authority to edit all group metadata (except for group id)
 - If the last user leaves a submitting group, the group becomes 'dangling'—it exists but is no longer accessible, and a new group with the same name cannot be created.
 - Admin users can manually delete a submitting group directly on the DB but must transfer ownership of sequence entries to another submitting group before doing so to fulfill the foreign key constraint.
 

backend/README.md

@@ -31,6 +31,8 @@ All commands mentioned in this section are run from the `backend` directory unle
    ./start_dev.sh
    ```
 
+The service listens, by default, to **port 8079**: <http://localhost:8079/swagger-ui/index.html>.
+
 3. Clean up the database when done:
 
    ```sh
@@ -67,8 +69,6 @@ You need to set:
 
 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.)
 
-The service listens, by default, to **port 8079**: <http://localhost:8079/swagger-ui/index.html>.
-
 Note: When using a postgresSQL development platform (e.g. pgAdmin) the hostname is 127.0.0.1 and not localhost - this is defined in the `deploy.py` file.
 
 Note that we also use flyway in the ena-submission pod to create an additional schema in the database, ena-submission. This schema is not added here.

backend/build.gradle

@@ -72,7 +72,25 @@ dependencies {
     }
 }
 
+// Check if the docker engine is running and reachable
+task checkDocker {
+    doLast {
+        def process = "docker info".execute()
+        def output = new StringWriter()
+        def error = new StringWriter()
+        process.consumeProcessOutput(output, error)
+        process.waitFor()
+
+        if (process.exitValue() != 0) {
+            throw new GradleException("Docker is not running: ${error.toString()}")
+        }
+        println "Docker is running."
+    }
+}
+
 tasks.named('test') {
+    // Docker is required to start the testing database
+    dependsOn checkDocker
     useJUnitPlatform()
     testLogging {
         events TestLogEvent.FAILED

backend/src/main/kotlin/org/loculus/backend/controller/GroupManagementController.kt

@@ -29,11 +29,24 @@ class GroupManagementController(private val groupManagementDatabaseService: Grou
     @PostMapping("/groups", produces = [MediaType.APPLICATION_JSON_VALUE])
     fun createNewGroup(
         @HiddenParam authenticatedUser: AuthenticatedUser,
-        @Parameter(description = "Information about the newly created group")
+        @Parameter(description = "Information about the newly created group.")
         @RequestBody
         group: NewGroup,
     ): Group = groupManagementDatabaseService.createNewGroup(group, authenticatedUser)
 
+    @Operation(description = "Edit a group. Only users part of the group can edit it. The updated group is returned.")
+    @ResponseStatus(HttpStatus.OK)
+    @PutMapping("/groups/{groupId}", produces = [MediaType.APPLICATION_JSON_VALUE])
+    fun editGroup(
+        @HiddenParam authenticatedUser: AuthenticatedUser,
+        @Parameter(
+            description = "The id of the group to edit.",
+        ) @PathVariable groupId: Int,
+        @Parameter(description = "Updated group properties.")
+        @RequestBody
+        group: NewGroup,
+    ): Group = groupManagementDatabaseService.updateGroup(groupId, group, authenticatedUser)
+
     @Operation(description = "Get details of a group.")
     @ResponseStatus(HttpStatus.OK)
     @GetMapping("/groups/{groupId}", produces = [MediaType.APPLICATION_JSON_VALUE])

backend/src/main/kotlin/org/loculus/backend/service/groupmanagement/GroupManagementDatabaseService.kt

@@ -32,35 +32,14 @@ class GroupManagementDatabaseService(
         val users = UserGroupEntity.find { UserGroupsTable.groupIdColumn eq groupId }
 
         return GroupDetails(
-            group = Group(
-                groupId = groupEntity.id.value,
-                groupName = groupEntity.groupName,
-                institution = groupEntity.institution,
-                address = Address(
-                    line1 = groupEntity.addressLine1,
-                    line2 = groupEntity.addressLine2,
-                    postalCode = groupEntity.addressPostalCode,
-                    city = groupEntity.addressCity,
-                    state = groupEntity.addressState,
-                    country = groupEntity.addressCountry,
-                ),
-                contactEmail = groupEntity.contactEmail,
-            ),
+            group = groupEntity.toGroup(),
             users = users.map { User(it.userName) },
         )
     }
 
     fun createNewGroup(group: NewGroup, authenticatedUser: AuthenticatedUser): Group {
         val groupEntity = GroupEntity.new {
-            groupName = group.groupName
-            institution = group.institution
-            addressLine1 = group.address.line1
-            addressLine2 = group.address.line2
-            addressPostalCode = group.address.postalCode
-            addressState = group.address.state
-            addressCity = group.address.city
-            addressCountry = group.address.country
-            contactEmail = group.contactEmail
+            this.updateWith(group)
         }
 
         val groupId = groupEntity.id.value
@@ -72,20 +51,21 @@ class GroupManagementDatabaseService(
 
         auditLogger.log(authenticatedUser.username, "Created group: ${group.groupName}")
 
-        return Group(
-            groupId = groupEntity.id.value,
-            groupName = groupEntity.groupName,
-            institution = groupEntity.institution,
-            address = Address(
-                line1 = groupEntity.addressLine1,
-                line2 = groupEntity.addressLine2,
-                postalCode = groupEntity.addressPostalCode,
-                city = groupEntity.addressCity,
-                state = groupEntity.addressState,
-                country = groupEntity.addressCountry,
-            ),
-            contactEmail = groupEntity.contactEmail,
-        )
+        return groupEntity.toGroup()
+    }
+
+    fun updateGroup(groupId: Int, group: NewGroup, authenticatedUser: AuthenticatedUser): Group {
+        groupManagementPreconditionValidator.validateThatUserExists(authenticatedUser.username)
+
+        groupManagementPreconditionValidator.validateUserIsAllowedToModifyGroup(groupId, authenticatedUser)
+
+        val groupEntity = GroupEntity.findById(groupId) ?: throw NotFoundException("Group $groupId does not exist.")
+
+        groupEntity.updateWith(group)
+
+        auditLogger.log(authenticatedUser.username, "Updated group: ${group.groupName}")
+
+        return groupEntity.toGroup()
     }
 
     fun getGroupsOfUser(authenticatedUser: AuthenticatedUser): List<Group> {
@@ -172,4 +152,31 @@ class GroupManagementDatabaseService(
                 contactEmail = it.contactEmail,
             )
         }
+
+    private fun GroupEntity.updateWith(group: NewGroup) {
+        groupName = group.groupName
+        institution = group.institution
+        addressLine1 = group.address.line1
+        addressLine2 = group.address.line2
+        addressPostalCode = group.address.postalCode
+        addressState = group.address.state
+        addressCity = group.address.city
+        addressCountry = group.address.country
+        contactEmail = group.contactEmail
+    }
+
+    private fun GroupEntity.toGroup(): Group = Group(
+        groupId = this.id.value,
+        groupName = this.groupName,
+        institution = this.institution,
+        address = Address(
+            line1 = this.addressLine1,
+            line2 = this.addressLine2,
+            postalCode = this.addressPostalCode,
+            city = this.addressCity,
+            state = this.addressState,
+            country = this.addressCountry,
+        ),
+        contactEmail = this.contactEmail,
+    )
 }

backend/src/test/kotlin/org/loculus/backend/controller/groupmanagement/GroupManagementControllerClient.kt

@@ -49,6 +49,14 @@ class GroupManagementControllerClient(private val mockMvc: MockMvc, private val
             .withAuth(jwt),
     )
 
+    fun updateGroup(groupId: Int, group: NewGroup = NEW_GROUP, jwt: String? = jwtForDefaultUser): ResultActions =
+        mockMvc.perform(
+            put("/groups/$groupId")
+                .contentType(MediaType.APPLICATION_JSON_VALUE)
+                .content(objectMapper.writeValueAsString(group))
+                .withAuth(jwt),
+        )
+
     fun getGroupsOfUser(jwt: String? = jwtForDefaultUser): ResultActions = mockMvc.perform(
         get("/user/groups").withAuth(jwt),
     )

backend/src/test/kotlin/org/loculus/backend/controller/groupmanagement/GroupManagementControllerTest.kt

@@ -11,6 +11,8 @@ import org.junit.jupiter.api.Test
 import org.junit.jupiter.params.ParameterizedTest
 import org.junit.jupiter.params.provider.MethodSource
 import org.keycloak.representations.idm.UserRepresentation
+import org.loculus.backend.api.Address
+import org.loculus.backend.api.NewGroup
 import org.loculus.backend.controller.ALTERNATIVE_DEFAULT_GROUP
 import org.loculus.backend.controller.ALTERNATIVE_DEFAULT_GROUP_NAME
 import org.loculus.backend.controller.ALTERNATIVE_DEFAULT_USER_NAME
@@ -104,6 +106,50 @@ class GroupManagementControllerTest(@Autowired private val client: GroupManageme
             .andExpect(jsonPath("\$.[0].contactEmail").value(NEW_GROUP.contactEmail))
     }
 
+    @Test
+    fun `GIVEN a group is created WHEN I edit the group THEN the group information is updated`() {
+        val groupId = client.createNewGroup(group = DEFAULT_GROUP, jwt = jwtForDefaultUser)
+            .andExpect(status().isOk)
+            .andGetGroupId()
+        val newInfo = NewGroup(
+            groupName = "Updated group name",
+            institution = "Updated institution",
+            address = Address(
+                line1 = "Updated address line 1",
+                line2 = "Updated address line 2",
+                postalCode = "Updated post code",
+                city = "Updated city",
+                state = "Updated state",
+                country = "Updated country",
+            ),
+            contactEmail = "Updated email",
+        )
+        client.updateGroup(groupId = groupId, group = newInfo, jwt = jwtForDefaultUser)
+            .andExpect(status().isOk)
+            .andExpect(content().contentType(MediaType.APPLICATION_JSON_VALUE))
+            .andExpect(jsonPath("\$.groupName").value(newInfo.groupName))
+            .andExpect(jsonPath("\$.institution").value(newInfo.institution))
+            .andExpect(jsonPath("\$.address.line1").value(newInfo.address.line1))
+            .andExpect(jsonPath("\$.address.line2").value(newInfo.address.line2))
+            .andExpect(jsonPath("\$.address.city").value(newInfo.address.city))
+            .andExpect(jsonPath("\$.address.state").value(newInfo.address.state))
+            .andExpect(jsonPath("\$.address.postalCode").value(newInfo.address.postalCode))
+            .andExpect(jsonPath("\$.address.country").value(newInfo.address.country))
+            .andExpect(jsonPath("\$.contactEmail").value(newInfo.contactEmail))
+        client.getDetailsOfGroup(groupId = groupId, jwt = jwtForDefaultUser)
+            .andExpect(status().isOk)
+            .andExpect(content().contentType(MediaType.APPLICATION_JSON_VALUE))
+            .andExpect(jsonPath("\$.group.groupName").value(newInfo.groupName))
+            .andExpect(jsonPath("\$.group.institution").value(newInfo.institution))
+            .andExpect(jsonPath("\$.group.address.line1").value(newInfo.address.line1))
+            .andExpect(jsonPath("\$.group.address.line2").value(newInfo.address.line2))
+            .andExpect(jsonPath("\$.group.address.city").value(newInfo.address.city))
+            .andExpect(jsonPath("\$.group.address.state").value(newInfo.address.state))
+            .andExpect(jsonPath("\$.group.address.postalCode").value(newInfo.address.postalCode))
+            .andExpect(jsonPath("\$.group.address.country").value(newInfo.address.country))
+            .andExpect(jsonPath("\$.group.contactEmail").value(newInfo.contactEmail))
+    }
+
     @Test
     fun `WHEN superuser queries groups of user THEN returns all groups`() {
         client.createNewGroup(group = DEFAULT_GROUP, jwt = jwtForDefaultUser)

ena-submission/README.md

@@ -37,6 +37,10 @@ In a loop:
   - else: set status to HAS_ERRORS and fill in errors
 - Get sequences in `project_table` in state HAS_ERRORS for over 15min and sequences in status SUBMITTING for over 15min: send slack notification
 
+##### Known limitations
+
+Group info can be updated in loculus after the project has been created in ENA. This is not currently handled by the pipeline. Issue: <https://github.com/loculus-project/loculus/issues/2939>
+
 #### create_sample
 
 Maps loculus metadata to ena metadata using template: https://www.ebi.ac.uk/ena/browser/view/ERC000033

ena-submission/scripts/call_loculus.py

@@ -27,7 +27,6 @@ class Config:
     keycloak_client_id: str
     username: str
     password: str
-    group_name: str
     ena_specific_metadata: list[str]
 
 

ena-submission/scripts/create_project.py

@@ -217,6 +217,7 @@ def submission_table_update(db_config: SimpleConnectionPool):
             raise RuntimeError(error_msg)
 
 
+# TODO Allow propagating updated group info https://github.com/loculus-project/loculus/issues/2939
 def project_table_create(
     db_config: SimpleConnectionPool, config: Config, retry_number: int = 3, test: bool = False
 ):

generate_local_test_config.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 set -e
 

get_testuser_token.sh

@@ -1,6 +1,12 @@
-#!/usr/bin/bash
+#!/usr/bin/env bash
 set -eu
 
+# Check if jq is installed
+if ! command -v jq &> /dev/null; then
+  echo "Error: jq is not installed. Please install it from https://jqlang.github.io/jq/"
+  exit 1
+fi
+
 KEYCLOAK_TOKEN_URL="http://localhost:8083/realms/loculus/protocol/openid-connect/token"
 KEYCLOAK_CLIENT_ID="backend-client"
 

ingest/config/defaults.yaml

@@ -70,7 +70,7 @@ column_mapping:
   Virus Name: ncbiVirusName
   Virus Pangolin Classification: ncbiVirusPangolin
   Virus Taxonomic ID: ncbiVirusTaxId
-group_name: insdc_ingest_group
+group_name: insdc_ingest_group  # Used only to set the group name, never read
 username: insdc_ingest_user
 password: insdc_ingest_user
 keycloak_client_id: backend-client

ingest/scripts/call_loculus.py

@@ -123,7 +123,7 @@ def make_request(  # noqa: PLR0913, PLR0917
     return response
 
 
-def create_group(config: Config) -> str:
+def create_group_and_return_group_id(config: Config) -> str:
     create_group_url = f"{backend_url(config)}/groups"
     group_name = config.group_name
 
@@ -151,7 +151,7 @@ def create_group(config: Config) -> str:
     return group_id
 
 
-def get_or_create_group(config: Config, allow_creation: bool = False) -> str:
+def get_or_create_group_and_return_group_id(config: Config, allow_creation: bool = False) -> str:
     """Returns group id"""
     get_user_groups_url = f"{backend_url(config)}/user/groups"
 
@@ -168,7 +168,7 @@ def get_or_create_group(config: Config, allow_creation: bool = False) -> str:
         raise ValueError(msg)
 
     logger.info("User is not in any group. Creating a new group")
-    return create_group(config)
+    return create_group_and_return_group_id(config)
 
 
 def submit_or_revise(
@@ -332,8 +332,10 @@ def get_submitted(config: Config):
         if len(entries) == expected_record_count:
             f"Got {len(entries)} records as expected"
             break
-        logger.error(f"Got incomplete original metadata stream: expected {len(entries)}"
-                        f"records but got {expected_record_count}. Retrying after 60 seconds.")
+        logger.error(
+            f"Got incomplete original metadata stream: expected {len(entries)}"
+            f"records but got {expected_record_count}. Retrying after 60 seconds."
+        )
         sleep(60)
 
     # Initialize the dictionary to store results
@@ -467,7 +469,9 @@ def record_factory(*args, **kwargs):
     if mode in {"submit", "revise"}:
         logging.info(f"Starting {mode}")
         try:
-            group_id = get_or_create_group(config, allow_creation=mode == "submit")
+            group_id = get_or_create_group_and_return_group_id(
+                config, allow_creation=mode == "submit"
+            )
         except ValueError as e:
             logger.error(f"Aborting {mode} due to error: {e}")
             return
@@ -487,7 +491,9 @@ def record_factory(*args, **kwargs):
 
     if mode == "regroup-and-revoke":
         try:
-            group_id = get_or_create_group(config, allow_creation=mode == "submit")
+            group_id = get_or_create_group_and_return_group_id(
+                config, allow_creation=mode == "submit"
+            )
         except ValueError as e:
             logger.error(f"Aborting {mode} due to error: {e}")
             return