feat(backend, website): Use version comments field for revocations as well.

backend/src/main/kotlin/org/loculus/backend/api/SubmissionTypes.kt

@@ -68,6 +68,17 @@ data class AccessionVersionsFilterWithDeletionScope(
     val scope: DeleteSequenceScope,
 )
 
+data class AccessionsToRevokeWithComment(
+    @Schema(
+        description = "List of accessions to revoke.",
+    )
+    val accessions: List<Accession>,
+    @Schema(
+        description = "Reason for revocation or other details, added as version_comment",
+    )
+    val versionComment: String? = null,
+)
+
 enum class ApproveDataScope {
     ALL,
     WITHOUT_WARNINGS,

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

@@ -15,7 +15,7 @@ import org.jetbrains.exposed.sql.transactions.transaction
 import org.loculus.backend.api.AccessionVersion
 import org.loculus.backend.api.AccessionVersionsFilterWithApprovalScope
 import org.loculus.backend.api.AccessionVersionsFilterWithDeletionScope
-import org.loculus.backend.api.Accessions
+import org.loculus.backend.api.AccessionsToRevokeWithComment
 import org.loculus.backend.api.CompressionFormat
 import org.loculus.backend.api.DataUseTerms
 import org.loculus.backend.api.DataUseTermsType
@@ -397,9 +397,10 @@ class SubmissionController(
     fun revoke(
         @PathVariable @Valid
         organism: Organism,
-        @RequestBody body: Accessions,
+        @RequestBody body: AccessionsToRevokeWithComment,
         @HiddenParam authenticatedUser: AuthenticatedUser,
-    ): List<SubmissionIdMapping> = submissionDatabaseService.revoke(body.accessions, authenticatedUser, organism)
+    ): List<SubmissionIdMapping> =
+        submissionDatabaseService.revoke(body.accessions, authenticatedUser, organism, body.versionComment)
 
     @Operation(description = DELETE_SEQUENCES_DESCRIPTION)
     @ResponseStatus(HttpStatus.OK)

backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt

@@ -71,7 +71,8 @@ class ReleasedDataModel(
             ("releasedDate" to TextNode(rawProcessedData.releasedAtTimestamp.toUtcDateString())) +
             ("versionStatus" to TextNode(siloVersionStatus.name)) +
             ("dataUseTerms" to TextNode(currentDataUseTerms.type.name)) +
-            ("dataUseTermsRestrictedUntil" to restrictedDataUseTermsUntil)
+            ("dataUseTermsRestrictedUntil" to restrictedDataUseTermsUntil) +
+            ("version_comment" to TextNode(rawProcessedData.versionComment))
 
         if (backendConfig.dataUseTermsUrls != null) {
             val url = if (rawProcessedData.dataUseTerms == DataUseTerms.Open) {

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

@@ -21,6 +21,7 @@ object SequenceEntriesTable : Table(SEQUENCE_ENTRIES_TABLE_NAME) {
 
     val accessionColumn = varchar("accession", 255)
     val versionColumn = long("version")
+    val versionCommentColumn = varchar("version_comment", 255).nullable()
     val organismColumn = varchar("organism", 255)
     val submissionIdColumn = varchar("submission_id", 255)
     val submitterColumn = varchar("submitter", 255)

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

@@ -40,6 +40,7 @@ object SequenceEntriesView : Table(SEQUENCE_ENTRIES_VIEW_NAME) {
     val releasedAtTimestampColumn = datetime("released_at").nullable()
     val statusColumn = varchar("status", 255)
     val isRevocationColumn = bool("is_revocation").default(false)
+    val versionCommentColumn = varchar("version_comment", 255).nullable()
     val errorsColumn = jacksonSerializableJsonb<List<PreprocessingAnnotation>>("errors").nullable()
     val warningsColumn = jacksonSerializableJsonb<List<PreprocessingAnnotation>>("warnings").nullable()
 

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

@@ -29,6 +29,7 @@ import org.jetbrains.exposed.sql.not
 import org.jetbrains.exposed.sql.notExists
 import org.jetbrains.exposed.sql.selectAll
 import org.jetbrains.exposed.sql.statements.StatementType
+import org.jetbrains.exposed.sql.stringParam
 import org.jetbrains.exposed.sql.transactions.transaction
 import org.jetbrains.exposed.sql.update
 import org.loculus.backend.api.AccessionVersion
@@ -538,6 +539,7 @@ class SubmissionDatabaseService(
             SequenceEntriesView.accessionColumn,
             SequenceEntriesView.versionColumn,
             SequenceEntriesView.isRevocationColumn,
+            SequenceEntriesView.versionCommentColumn,
             SequenceEntriesView.jointDataColumn,
             SequenceEntriesView.submitterColumn,
             SequenceEntriesView.groupIdColumn,
@@ -577,6 +579,7 @@ class SubmissionDatabaseService(
                     DataUseTermsType.fromString(it[DataUseTermsTable.dataUseTermsTypeColumn]),
                     it[DataUseTermsTable.restrictedUntilColumn],
                 ),
+                versionComment = it[SequenceEntriesView.versionCommentColumn],
             )
         }
 
@@ -673,6 +676,7 @@ class SubmissionDatabaseService(
         accessions: List<Accession>,
         authenticatedUser: AuthenticatedUser,
         organism: Organism,
+        versionComment: String?,
     ): List<SubmissionIdMapping> {
         log.info { "revoking ${accessions.size} sequences" }
 
@@ -682,30 +686,35 @@ class SubmissionDatabaseService(
                 .andThatSequenceEntriesAreInStates(listOf(Status.APPROVED_FOR_RELEASE))
                 .andThatOrganismIs(organism)
         }
-
         val now = Clock.System.now().toLocalDateTime(TimeZone.UTC)
+
         SequenceEntriesTable.insert(
-            SequenceEntriesTable
-                .select(
-                    SequenceEntriesTable.accessionColumn,
-                    SequenceEntriesTable.versionColumn.plus(1),
-                    SequenceEntriesTable.submissionIdColumn,
-                    SequenceEntriesTable.submitterColumn,
-                    SequenceEntriesTable.groupIdColumn,
-                    dateTimeParam(now),
-                    booleanParam(true),
-                    SequenceEntriesTable.organismColumn,
-                )
-                .where {
-                    (SequenceEntriesTable.accessionColumn inList accessions) and
-                        SequenceEntriesTable.isMaxVersion
+            SequenceEntriesTable.select(
+                SequenceEntriesTable.accessionColumn, SequenceEntriesTable.versionColumn.plus(1),
+                when (versionComment) {
+                    null -> Op.nullOp()
+                    else -> stringParam(versionComment)
                 },
+                SequenceEntriesTable.submissionIdColumn,
+                SequenceEntriesTable.submitterColumn,
+                SequenceEntriesTable.groupIdColumn,
+                dateTimeParam(
+                    now,
+                ),
+                booleanParam(true), SequenceEntriesTable.organismColumn,
+            ).where {
+                (
+                    SequenceEntriesTable.accessionColumn inList
+                        accessions
+                    ) and
+                    SequenceEntriesTable.isMaxVersion
+            },
             columns = listOf(
                 SequenceEntriesTable.accessionColumn,
                 SequenceEntriesTable.versionColumn,
+                SequenceEntriesTable.versionCommentColumn,
                 SequenceEntriesTable.submissionIdColumn,
-                SequenceEntriesTable.submitterColumn,
-                SequenceEntriesTable.groupIdColumn,
+                SequenceEntriesTable.submitterColumn, SequenceEntriesTable.groupIdColumn,
                 SequenceEntriesTable.submittedAtTimestampColumn,
                 SequenceEntriesTable.isRevocationColumn,
                 SequenceEntriesTable.organismColumn,
@@ -1017,6 +1026,7 @@ data class RawProcessedData(
     override val accession: Accession,
     override val version: Version,
     val isRevocation: Boolean,
+    val versionComment: String?,
     val submitter: String,
     val groupId: Int,
     val groupName: String,

backend/src/main/resources/db/migration/V1__init.sql

@@ -24,6 +24,7 @@ values (1, now());
 create table sequence_entries (
     accession text not null,
     version bigint not null,
+    version_comment text,
     organism text not null,
     submission_id text not null,
     submitter text not null,
@@ -134,6 +135,7 @@ from
 create table metadata_upload_aux_table (
     accession text,
     version bigint,
+    version_comment text,
     upload_id text not null,
     organism text not null,
     submission_id text not null,

backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt

@@ -106,6 +106,7 @@ class GetReleasedDataEndpointTest(
                 "releasedDate" to TextNode(Clock.System.now().toLocalDateTime(TimeZone.UTC).date.toString()),
                 "submittedDate" to TextNode(Clock.System.now().toLocalDateTime(TimeZone.UTC).date.toString()),
                 "dataUseTermsRestrictedUntil" to NullNode.getInstance(),
+                "version_comment" to NullNode.getInstance(),
                 "booleanColumn" to BooleanNode.TRUE,
             )
 
@@ -214,10 +215,17 @@ class GetReleasedDataEndpointTest(
                     value,
                     `is`(TextNode(Clock.System.now().toLocalDateTime(TimeZone.UTC).date.toString())),
                 )
+
                 "releasedDate" -> assertThat(
                     value,
                     `is`(TextNode(Clock.System.now().toLocalDateTime(TimeZone.UTC).date.toString())),
                 )
+
+                "version_comment" -> assertThat(
+                    value,
+                    `is`(TextNode("This is a test revocation")),
+                )
+
                 else -> assertThat("value for $key", value, `is`(NullNode.instance))
             }
         }

backend/src/test/kotlin/org/loculus/backend/controller/submission/SubmissionControllerClient.kt

@@ -178,10 +178,17 @@ class SubmissionControllerClient(private val mockMvc: MockMvc, private val objec
         listOfSequenceEntriesToRevoke: List<Accession>,
         organism: String = DEFAULT_ORGANISM,
         jwt: String? = jwtForDefaultUser,
+        versionComment: String? = null,
     ): ResultActions = mockMvc.perform(
         post(addOrganismToPath("/revoke", organism = organism))
             .contentType(MediaType.APPLICATION_JSON)
-            .content("""{"accessions":${objectMapper.writeValueAsString(listOfSequenceEntriesToRevoke)}}""")
+            .content(
+                """{"accessions":${
+                    objectMapper.writeValueAsString(
+                        listOfSequenceEntriesToRevoke,
+                    )
+                }, "versionComment":$versionComment"}""",
+            )
             .withAuth(jwt),
     )
 

backend/src/test/kotlin/org/loculus/backend/controller/submission/SubmissionConvenienceClient.kt

@@ -196,7 +196,14 @@ class SubmissionConvenienceClient(
 
     fun prepareRevokedSequenceEntries(organism: String = DEFAULT_ORGANISM): List<AccessionVersionInterface> {
         val accessionVersions = prepareDataTo(Status.APPROVED_FOR_RELEASE, organism = organism)
-        val revocationVersions = revokeSequenceEntries(accessionVersions.map { it.accession }, organism = organism)
+        val revocationVersions =
+            revokeSequenceEntries(
+                accessionVersions.map {
+                    it.accession
+                },
+                organism = organism,
+                versionComment = "This is a test revocation",
+            )
         return approveProcessedSequenceEntries(revocationVersions, organism = organism)
     }
 
@@ -323,11 +330,13 @@ class SubmissionConvenienceClient(
         listOfAccessionsToRevoke: List<Accession>,
         organism: String = DEFAULT_ORGANISM,
         username: String = DEFAULT_USER_NAME,
+        versionComment: String? = null,
     ): List<SubmissionIdMapping> = deserializeJsonResponse(
         client.revokeSequenceEntries(
             listOfAccessionsToRevoke,
             organism = organism,
             jwt = generateJwtFor(username),
+            versionComment = versionComment,
         ),
     )
 

website/src/components/SequenceDetailsPage/RevokeButton.tsx

@@ -1,12 +1,12 @@
-import { type FC } from 'react';
+import { type FC, useState } from 'react';
+import { confirmAlert } from 'react-confirm-alert';
 import { toast } from 'react-toastify';
 
 import { routes } from '../../routes/routes';
 import { backendClientHooks } from '../../services/serviceHooks';
 import type { ClientConfig } from '../../types/runtimeConfig';
 import { createAuthorizationHeader } from '../../utils/createAuthorizationHeader';
 import { stringifyMaybeAxiosError } from '../../utils/stringifyMaybeAxiosError';
-import { displayConfirmationDialog } from '../ConfirmationDialog';
 import { withQueryProvider } from '../common/withQueryProvider';
 
 type RevokeSequenceEntryProps = {
@@ -26,7 +26,10 @@ const InnerRevokeButton: FC<RevokeSequenceEntryProps> = ({
 }) => {
     const hooks = backendClientHooks(clientConfig);
     const useRevokeSequenceEntries = hooks.useRevokeSequences(
-        { headers: createAuthorizationHeader(accessToken), params: { organism } },
+        {
+            headers: createAuthorizationHeader(accessToken),
+            params: { organism },
+        },
         {
             onSuccess: () => {
                 document.location = routes.userSequenceReviewPage(organism, groupId);
@@ -39,15 +42,15 @@ const InnerRevokeButton: FC<RevokeSequenceEntryProps> = ({
         },
     );
 
-    const handleRevokeSequenceEntry = () => {
-        useRevokeSequenceEntries.mutate({ accessions: [accessionVersion] });
+    const handleRevokeSequenceEntry = (inputValue: string) => {
+        useRevokeSequenceEntries.mutate({ accessions: [accessionVersion], versionComment: inputValue });
     };
 
     return (
         <button
             className='btn btn-sm  bg-red-400'
             onClick={() =>
-                displayConfirmationDialog({
+                displayRevocationDialog({
                     dialogText: 'Are you sure you want to create a revocation for this sequence?',
                     onConfirmation: handleRevokeSequenceEntry,
                 })
@@ -58,6 +61,77 @@ const InnerRevokeButton: FC<RevokeSequenceEntryProps> = ({
     );
 };
 
+interface DisplayRevocationProps {
+    dialogText: string;
+    onConfirmation: (inputValue: string) => void;
+}
+
+export const displayRevocationDialog = ({ dialogText, onConfirmation }: DisplayRevocationProps) => {
+    confirmAlert({
+        closeOnClickOutside: true,
+
+        customUI: ({ onClose }) => (
+            <RevocationDialog
+                dialogText={dialogText}
+                onConfirmation={async (inputValue) => {
+                    await onConfirmation(inputValue);
+                    onClose();
+                }}
+                onClose={onClose}
+            />
+        ),
+    });
+};
+
+interface RevocationDialogProps {
+    dialogText: string;
+    onConfirmation: (inputValue: string) => void;
+    onClose: () => void;
+}
+
+export const RevocationDialog: React.FC<RevocationDialogProps> = ({ dialogText, onConfirmation, onClose }) => {
+    const [inputValue, setInputValue] = useState('');
+
+    return (
+        <div className='modal-box'>
+            <form method='dialog'>
+                <button className='btn btn-sm btn-circle btn-ghost absolute right-2 top-2' onClick={onClose}>
+                    ✕
+                </button>
+            </form>
+
+            <h3 className='font-bold text-lg'>{dialogText}</h3>
+
+            <input
+                type='text'
+                value={inputValue}
+                onChange={(e) => setInputValue(e.target.value)}
+                placeholder='Enter reason for revocation'
+                className='mt-4 w-11/12 mx-auto block'
+            />
+
+            <div className='flex justify-end gap-4 mt-4'>
+                <form method='dialog'>
+                    <button className='btn loculusColor text-white hover:bg-primary-700' onClick={onClose}>
+                        Cancel
+                    </button>
+                </form>
+                <form method='dialog'>
+                    <button
+                        className='btn loculusColor text-white hover:bg-primary-700'
+                        onClick={(e) => {
+                            e.preventDefault();
+                            onConfirmation(inputValue);
+                        }}
+                    >
+                        Confirm
+                    </button>
+                </form>
+            </div>
+        </div>
+    );
+};
+
 export const RevokeButton = withQueryProvider(InnerRevokeButton);
 
 function getRevokeSequenceEntryErrorMessage(error: unknown) {