feat: Edit group info (#2854)

Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>
Co-authored-by: Loculus bot <bot@loculus.org>

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.
@@ -85,7 +85,10 @@ When running the backend behind a proxy, the proxy needs to set X-Forwarded head
 
 ### Run tests and lints
 
-The tests use Testcontainers to start a PostgreSQL database. This requires Docker or a Docker-API compatible container runtime to be installed, and the user executing the test needs the necessary permissions to use it. See [the documentation of the Testcontainers](https://java.testcontainers.org/supported_docker_environment/) for details.
+The tests use [Testcontainers](https://testcontainers.com/) to start a PostgreSQL database.
+This requires Docker or a Docker-API compatible container runtime to be installed and running,
+and the user executing the test needs the necessary permissions to use it.
+See [the documentation of the Testcontainers](https://java.testcontainers.org/supported_docker_environment/) for details.
 
 ```bash
 ./gradlew test
@@ -97,7 +100,7 @@ The tests use Testcontainers to start a PostgreSQL database. This requires Docke
 ./gradlew ktlintCheck
 ```
 
-## Format
+### Format
 
 ```bash
 ./gradlew ktlintFormat

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 with https://java.testcontainers.org/
+    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/model/ReleasedDataModel.kt

@@ -12,7 +12,14 @@ import org.loculus.backend.api.Organism
 import org.loculus.backend.api.ProcessedData
 import org.loculus.backend.api.VersionStatus
 import org.loculus.backend.config.BackendConfig
+import org.loculus.backend.service.groupmanagement.GROUPS_TABLE_NAME
+import org.loculus.backend.service.submission.CURRENT_PROCESSING_PIPELINE_TABLE_NAME
+import org.loculus.backend.service.submission.EXTERNAL_METADATA_TABLE_NAME
+import org.loculus.backend.service.submission.METADATA_UPLOAD_AUX_TABLE_NAME
 import org.loculus.backend.service.submission.RawProcessedData
+import org.loculus.backend.service.submission.SEQUENCE_ENTRIES_PREPROCESSED_DATA_TABLE_NAME
+import org.loculus.backend.service.submission.SEQUENCE_ENTRIES_TABLE_NAME
+import org.loculus.backend.service.submission.SEQUENCE_UPLOAD_AUX_TABLE_NAME
 import org.loculus.backend.service.submission.SubmissionDatabaseService
 import org.loculus.backend.service.submission.UpdateTrackerTable
 import org.loculus.backend.utils.Accession
@@ -27,12 +34,13 @@ private val log = KotlinLogging.logger { }
 
 val RELEASED_DATA_RELATED_TABLES: List<String> =
     listOf(
-        "sequence_entries",
-        "sequence_entries_preprocessed_data",
-        "external_metadata",
-        "current_processing_pipeline",
-        "metadata_upload_aux_table",
-        "sequence_upload_aux_table",
+        CURRENT_PROCESSING_PIPELINE_TABLE_NAME,
+        EXTERNAL_METADATA_TABLE_NAME,
+        GROUPS_TABLE_NAME,
+        METADATA_UPLOAD_AUX_TABLE_NAME,
+        SEQUENCE_ENTRIES_TABLE_NAME,
+        SEQUENCE_ENTRIES_PREPROCESSED_DATA_TABLE_NAME,
+        SEQUENCE_UPLOAD_AUX_TABLE_NAME,
     )
 
 @Service

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/main/kotlin/org/loculus/backend/service/submission/CurrentProcessingPipelineTable.kt

@@ -3,9 +3,9 @@ package org.loculus.backend.service.submission
 import org.jetbrains.exposed.sql.Table
 import org.jetbrains.exposed.sql.kotlin.datetime.datetime
 
-const val CURRENT_PROCESSING_PIPELINE_TABLE = "current_processing_pipeline"
+const val CURRENT_PROCESSING_PIPELINE_TABLE_NAME = "current_processing_pipeline"
 
-object CurrentProcessingPipelineTable : Table(CURRENT_PROCESSING_PIPELINE_TABLE) {
+object CurrentProcessingPipelineTable : Table(CURRENT_PROCESSING_PIPELINE_TABLE_NAME) {
     val versionColumn = long("version")
     val startedUsingAtColumn = datetime("started_using_at")
 }

backend/src/main/kotlin/org/loculus/backend/service/submission/MetadataUploadAuxTable.kt

@@ -4,9 +4,9 @@ import org.jetbrains.exposed.sql.Table
 import org.jetbrains.exposed.sql.kotlin.datetime.datetime
 import org.loculus.backend.service.jacksonSerializableJsonb
 
-const val METADATA_UPLOAD_TABLE_NAME = "metadata_upload_aux_table"
+const val METADATA_UPLOAD_AUX_TABLE_NAME = "metadata_upload_aux_table"
 
-object MetadataUploadAuxTable : Table(METADATA_UPLOAD_TABLE_NAME) {
+object MetadataUploadAuxTable : Table(METADATA_UPLOAD_AUX_TABLE_NAME) {
     val accessionColumn = varchar("accession", 255).nullable()
     val versionColumn = long("version").nullable()
     val uploadIdColumn = varchar("upload_id", 255)

backend/src/main/kotlin/org/loculus/backend/service/submission/SequenceUploadAuxTable.kt

@@ -3,9 +3,9 @@ package org.loculus.backend.service.submission
 import org.jetbrains.exposed.sql.Table
 import org.loculus.backend.service.jacksonSerializableJsonb
 
-const val SEQUENCE_UPLOAD_TABLE_NAME = "sequence_upload_aux_table"
+const val SEQUENCE_UPLOAD_AUX_TABLE_NAME = "sequence_upload_aux_table"
 
-object SequenceUploadAuxTable : Table(SEQUENCE_UPLOAD_TABLE_NAME) {
+object SequenceUploadAuxTable : Table(SEQUENCE_UPLOAD_AUX_TABLE_NAME) {
     val sequenceUploadIdColumn = varchar("upload_id", 255)
     val sequenceSubmissionIdColumn = varchar("submission_id", 255)
     val segmentNameColumn = varchar("segment_name", 255)

backend/src/test/kotlin/org/loculus/backend/controller/EndpointTestExtension.kt

@@ -18,11 +18,11 @@ import org.loculus.backend.controller.submission.SubmissionConvenienceClient
 import org.loculus.backend.service.datauseterms.DATA_USE_TERMS_TABLE_NAME
 import org.loculus.backend.service.groupmanagement.GROUPS_TABLE_NAME
 import org.loculus.backend.service.groupmanagement.USER_GROUPS_TABLE_NAME
-import org.loculus.backend.service.submission.CURRENT_PROCESSING_PIPELINE_TABLE
-import org.loculus.backend.service.submission.METADATA_UPLOAD_TABLE_NAME
+import org.loculus.backend.service.submission.CURRENT_PROCESSING_PIPELINE_TABLE_NAME
+import org.loculus.backend.service.submission.METADATA_UPLOAD_AUX_TABLE_NAME
 import org.loculus.backend.service.submission.SEQUENCE_ENTRIES_PREPROCESSED_DATA_TABLE_NAME
 import org.loculus.backend.service.submission.SEQUENCE_ENTRIES_TABLE_NAME
-import org.loculus.backend.service.submission.SEQUENCE_UPLOAD_TABLE_NAME
+import org.loculus.backend.service.submission.SEQUENCE_UPLOAD_AUX_TABLE_NAME
 import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
 import org.springframework.boot.test.context.SpringBootTest
 import org.springframework.context.annotation.Import
@@ -54,6 +54,7 @@ private const val SPRING_DATASOURCE_PASSWORD = "spring.datasource.password"
 
 const val ACCESSION_SEQUENCE_NAME = "accession_sequence"
 const val DEFAULT_GROUP_NAME = "testGroup"
+const val DEFAULT_GROUP_NAME_CHANGED = "testGroup name updated"
 val DEFAULT_GROUP = NewGroup(
     groupName = DEFAULT_GROUP_NAME,
     institution = "testInstitution",
@@ -67,6 +68,19 @@ val DEFAULT_GROUP = NewGroup(
     ),
     contactEmail = "testEmail",
 )
+val DEFAULT_GROUP_CHANGED = NewGroup(
+    groupName = DEFAULT_GROUP_NAME_CHANGED,
+    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",
+)
 
 const val DEFAULT_USER_NAME = "testuser"
 const val SUPER_USER_NAME = "test_superuser"
@@ -162,12 +176,12 @@ class EndpointTestExtension :
 
 private fun clearDatabaseStatement(): String = """
         truncate table $GROUPS_TABLE_NAME cascade;
-        update $CURRENT_PROCESSING_PIPELINE_TABLE set version = 1, started_using_at = now();
+        update $CURRENT_PROCESSING_PIPELINE_TABLE_NAME set version = 1, started_using_at = now();
         truncate table $SEQUENCE_ENTRIES_TABLE_NAME;
         truncate table $SEQUENCE_ENTRIES_PREPROCESSED_DATA_TABLE_NAME;
         alter sequence $ACCESSION_SEQUENCE_NAME restart with 1;
         truncate table $USER_GROUPS_TABLE_NAME;
-        truncate $METADATA_UPLOAD_TABLE_NAME;
-        truncate $SEQUENCE_UPLOAD_TABLE_NAME;
+        truncate $METADATA_UPLOAD_AUX_TABLE_NAME;
+        truncate $SEQUENCE_UPLOAD_AUX_TABLE_NAME;
         truncate table $DATA_USE_TERMS_TABLE_NAME cascade;
     """

backend/src/test/kotlin/org/loculus/backend/controller/RequestAuthorization.kt

@@ -13,6 +13,7 @@ import java.util.Date
 val keyPair: KeyPair = Jwts.SIG.RS256.keyPair().build()
 
 val jwtForDefaultUser = generateJwtFor(DEFAULT_USER_NAME)
+val jwtForAlternativeUser = generateJwtFor(ALTERNATIVE_DEFAULT_USER_NAME)
 val jwtForProcessingPipeline = generateJwtFor("preprocessing_pipeline", listOf(PREPROCESSING_PIPELINE))
 val jwtForExternalMetadataUpdatePipeline =
     generateJwtFor("external_metadata_updater", listOf(EXTERNAL_METADATA_UPDATER))

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

@@ -13,6 +13,9 @@ import org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delet
 import org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get
 import org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post
 import org.springframework.test.web.servlet.request.MockMvcRequestBuilders.put
+import org.springframework.test.web.servlet.result.MockMvcResultMatchers.content
+import org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath
+import org.springframework.test.web.servlet.result.MockMvcResultMatchers.status
 
 const val NEW_GROUP_NAME = "newGroup"
 val NEW_GROUP = NewGroup(
@@ -49,6 +52,14 @@ 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/$groupId")
+                .contentType(MediaType.APPLICATION_JSON_VALUE)
+                .content(objectMapper.writeValueAsString(group))
+                .withAuth(jwt),
+        )
+
     fun getGroupsOfUser(jwt: String? = jwtForDefaultUser): ResultActions = mockMvc.perform(
         get("/user/groups").withAuth(jwt),
     )
@@ -74,3 +85,15 @@ fun ResultActions.andGetGroupId(): Int = andReturn()
     .response
     .contentAsString
     .let { JsonPath.read(it, "\$.groupId") }!!
+
+fun ResultActions.verifyGroupInfo(groupPath: String, expectedGroup: NewGroup) = andExpect(status().isOk())
+    .andExpect(content().contentType(MediaType.APPLICATION_JSON_VALUE))
+    .andExpect(jsonPath("$groupPath.groupName").value(expectedGroup.groupName))
+    .andExpect(jsonPath("$groupPath.institution").value(expectedGroup.institution))
+    .andExpect(jsonPath("$groupPath.address.line1").value(expectedGroup.address.line1))
+    .andExpect(jsonPath("$groupPath.address.line2").value(expectedGroup.address.line2))
+    .andExpect(jsonPath("$groupPath.address.city").value(expectedGroup.address.city))
+    .andExpect(jsonPath("$groupPath.address.state").value(expectedGroup.address.state))
+    .andExpect(jsonPath("$groupPath.address.postalCode").value(expectedGroup.address.postalCode))
+    .andExpect(jsonPath("$groupPath.address.country").value(expectedGroup.address.country))
+    .andExpect(jsonPath("$groupPath.contactEmail").value(expectedGroup.contactEmail))