wip: Seq page revocation

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

@@ -239,7 +239,7 @@ class SubmissionDatabaseService(
             accessionPreconditionValidator.validateAccessionVersions(
                 submitter,
                 accessionVersionsFilter,
-                listOf(AWAITING_APPROVAL),
+                listOf(AWAITING_APPROVAL, AWAITING_APPROVAL_FOR_REVOCATION),
                 organism,
             )
         }
@@ -255,7 +255,7 @@ class SubmissionDatabaseService(
                         (DataUseTermsTable.isNewestDataUseTerms)
                 },
             ).select {
-                val statusCondition = table.statusIs(AWAITING_APPROVAL)
+                val statusCondition = table.statusIsOneOf(listOf(AWAITING_APPROVAL, AWAITING_APPROVAL_FOR_REVOCATION))
 
                 val accessionCondition = if (accessionVersionsFilter !== null) {
                     table.accessionVersionIsIn(accessionVersionsFilter)

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

@@ -9,6 +9,7 @@ import org.loculus.backend.api.AccessionVersion
 import org.loculus.backend.api.ApproveDataScope
 import org.loculus.backend.api.Status.APPROVED_FOR_RELEASE
 import org.loculus.backend.api.Status.AWAITING_APPROVAL
+import org.loculus.backend.api.Status.AWAITING_APPROVAL_FOR_REVOCATION
 import org.loculus.backend.api.Status.IN_PROCESSING
 import org.loculus.backend.controller.DEFAULT_ORGANISM
 import org.loculus.backend.controller.EndpointTest
@@ -156,7 +157,8 @@ class ApproveProcessedDataEndpointTest(
                 jsonPath(
                     "$.detail",
                     containsString(
-                        "Accession versions are in not in one of the states [$AWAITING_APPROVAL]: " +
+                        "Accession versions are in not in one of the states " +
+                            "[$AWAITING_APPROVAL, $AWAITING_APPROVAL_FOR_REVOCATION]: " +
                             "${accessionVersionNotInCorrectState.first().displayAccessionVersion()} - $IN_PROCESSING",
                     ),
                 ),

website/package.json

@@ -43,6 +43,7 @@
     "react-chartjs-2": "^5.2.0",
     "react-confirm-alert": "^3.0.6",
     "react-dom": "^18.2.0",
+    "react-toastify": "^10.0.4",
     "react-tooltip": "^5.26.3",
     "unplugin-icons": "^0.18.5",
     "winston": "^3.11.0",

website/playwright.config.ts

@@ -20,17 +20,19 @@ export default defineConfig({
     globalSetup: './tests/playwrightSetup.ts',
 
     projects: [
+
         {
             name: 'chromium',
             use: { ...devices['Desktop Chrome'] },
         },
-        {
+        ...process.env.ALL_BROWSERS === 'true' ? [{
             name: 'firefox',
             use: { ...devices['Desktop Firefox'] },
         },
         {
             name: 'webkit',
             use: { ...devices['Desktop Safari'] },
-        },
+        }] : [],
+
     ],
-});
+});

website/src/components/ReviewPage/ReviewCard.tsx

@@ -4,6 +4,7 @@ import { Tooltip } from 'react-tooltip';
 import { backendClientHooks } from '../../services/serviceHooks.ts';
 import {
     awaitingApprovalStatus,
+    awaitingApprovalForRevocationStatus,
     type DataUseTerms,
     hasErrorsStatus,
     inProcessingStatus,
@@ -65,6 +66,14 @@ export const ReviewCard: FC<ReviewCardProps> = ({
                         value={sequenceEntryStatus.submissionId}
                     />
                     {data !== undefined && <MetadataList data={data} isLoading={isLoading} />}
+                    {sequenceEntryStatus.status === awaitingApprovalForRevocationStatus && (
+                        <KeyValueComponent
+                            accessionVersion={getAccessionVersionString(sequenceEntryStatus)}
+                            keyName='Revocation entry'
+                            value='This is a revocation entry, which will create a new version that revokes this accession'
+                            extraStyle='text-red-600 font-semibold'
+                        />
+                    )}
                 </div>
                 <ButtonBar
                     sequenceEntryStatus={sequenceEntryStatus}
@@ -105,39 +114,47 @@ const ButtonBar: FC<ButtonBarProps> = ({
     return (
         <div className='flex space-x-1 mb-auto pt-3.5'>
             <button
-                className={buttonBarClass(sequenceEntryStatus.status !== awaitingApprovalStatus)}
+                className={buttonBarClass(
+                    sequenceEntryStatus.status !== awaitingApprovalStatus &&
+                        sequenceEntryStatus.status !== awaitingApprovalForRevocationStatus,
+                )}
                 onClick={approveAccessionVersion}
                 data-tooltip-id={'approve-tooltip' + sequenceEntryStatus.accession}
-                disabled={sequenceEntryStatus.status !== awaitingApprovalStatus}
+                disabled={
+                    sequenceEntryStatus.status !== awaitingApprovalStatus &&
+                    sequenceEntryStatus.status !== awaitingApprovalForRevocationStatus
+                }
             >
                 <WpfPaperPlane />
             </button>
             <Tooltip
                 id={'approve-tooltip' + sequenceEntryStatus.accession}
                 content={
-                    sequenceEntryStatus.status === awaitingApprovalStatus
+                    sequenceEntryStatus.status === awaitingApprovalStatus ||
+                    sequenceEntryStatus.status === awaitingApprovalForRevocationStatus
                         ? 'Release this sequence entry'
                         : sequenceEntryStatus.status === hasErrorsStatus
-                          ? 'Cannot release. Fix Errors!'
-                          : 'Cannot release. Wait for preprocessing!'
+                          ? 'You need to fix the errors before releasing this sequence entry'
+                          : 'Still awaiting preprocessing'
                 }
             />
-
-            <button
-                className={buttonBarClass(
-                    sequenceEntryStatus.status !== hasErrorsStatus &&
-                        sequenceEntryStatus.status !== awaitingApprovalStatus,
-                )}
-                data-testid={`${getAccessionVersionString({ ...sequenceEntryStatus })}.edit`}
-                data-tooltip-id={'edit-tooltip' + sequenceEntryStatus.accession}
-                onClick={editAccessionVersion}
-                disabled={
-                    sequenceEntryStatus.status !== hasErrorsStatus &&
-                    sequenceEntryStatus.status !== awaitingApprovalStatus
-                }
-            >
-                <ClarityNoteEditLine />
-            </button>
+            {sequenceEntryStatus.status !== awaitingApprovalForRevocationStatus && (
+                <button
+                    className={buttonBarClass(
+                        sequenceEntryStatus.status !== hasErrorsStatus &&
+                            sequenceEntryStatus.status !== awaitingApprovalStatus,
+                    )}
+                    data-testid={`${getAccessionVersionString({ ...sequenceEntryStatus })}.edit`}
+                    data-tooltip-id={'edit-tooltip' + sequenceEntryStatus.accession}
+                    onClick={editAccessionVersion}
+                    disabled={
+                        sequenceEntryStatus.status !== hasErrorsStatus &&
+                        sequenceEntryStatus.status !== awaitingApprovalStatus
+                    }
+                >
+                    <ClarityNoteEditLine />
+                </button>
+            )}
             <Tooltip
                 id={'edit-tooltip' + sequenceEntryStatus.accession}
                 content={
@@ -151,13 +168,15 @@ const ButtonBar: FC<ButtonBarProps> = ({
             <button
                 className={buttonBarClass(
                     sequenceEntryStatus.status !== hasErrorsStatus &&
-                        sequenceEntryStatus.status !== awaitingApprovalStatus,
+                        sequenceEntryStatus.status !== awaitingApprovalStatus &&
+                        sequenceEntryStatus.status !== awaitingApprovalForRevocationStatus,
                 )}
                 onClick={deleteAccessionVersion}
                 data-tooltip-id={'delete-tooltip' + sequenceEntryStatus.accession}
                 disabled={
                     sequenceEntryStatus.status !== hasErrorsStatus &&
-                    sequenceEntryStatus.status !== awaitingApprovalStatus
+                    sequenceEntryStatus.status !== awaitingApprovalStatus &&
+                    sequenceEntryStatus.status !== awaitingApprovalForRevocationStatus
                 }
             >
                 <BiTrash />
@@ -166,7 +185,8 @@ const ButtonBar: FC<ButtonBarProps> = ({
                 id={'delete-tooltip' + sequenceEntryStatus.accession}
                 content={
                     sequenceEntryStatus.status !== hasErrorsStatus &&
-                    sequenceEntryStatus.status !== awaitingApprovalStatus
+                    sequenceEntryStatus.status !== awaitingApprovalStatus &&
+                    sequenceEntryStatus.status !== awaitingApprovalForRevocationStatus
                         ? 'Cannot discard. Wait for preprocessing.'
                         : 'Discard this sequence entry'
                 }

website/src/components/ReviewPage/ReviewPage.spec.tsx

@@ -117,13 +117,13 @@ describe('ReviewPage', () => {
         getByText('Discard sequences').click();
 
         await waitFor(() => {
-            expect(getByText((text) => text.includes('Discard 1 sequences with errors'))).toBeDefined();
-            expect(getByText((text) => text.includes('Release 1 sequences without errors'))).toBeDefined();
+            expect(getByText((text) => text.includes('Discard 1 sequence with errors'))).toBeDefined();
+            expect(getByText((text) => text.includes('Release 1 valid sequence'))).toBeDefined();
         });
 
         mockRequest.backend.getSequences(200, generateGetSequencesResponse([]));
 
-        getByText((text) => text.includes('Release 1 sequences without errors')).click();
+        getByText((text) => text.includes('Release 1 valid sequence')).click();
         await waitFor(() => {
             expect(getByText('Confirm')).toBeDefined();
         });

website/src/components/ReviewPage/ReviewPage.tsx

@@ -12,6 +12,7 @@ import {
     deleteProcessedDataWithErrorsScope,
     hasErrorsStatus,
     inProcessingStatus,
+    awaitingApprovalForRevocationStatus,
     type PageQuery,
     type SequenceEntryStatus,
 } from '../../types/backend.ts';
@@ -64,12 +65,16 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, accessTo
     const processingCount = hooks.getSequences.data.statusCounts[inProcessingStatus];
     const processedCount = hooks.getSequences.data.statusCounts[awaitingApprovalStatus];
     const errorCount = hooks.getSequences.data.statusCounts[hasErrorsStatus];
+    const revocationCount = hooks.getSequences.data.statusCounts[awaitingApprovalForRevocationStatus];
+
+    const finishedCount = processedCount + errorCount + revocationCount;
+
     const sequences: SequenceEntryStatus[] = hooks.getSequences.data.sequenceEntries;
 
     const controlPanel = (
         <div className='flex flex-col py-2'>
             <div>
-                {processedCount + errorCount} of {total} sequences processed.
+                {finishedCount} of {total} sequences processed.
                 {processingCount > 0 && <span className='loading loading-spinner loading-sm ml-3'> </span>}
             </div>
             <div>
@@ -112,7 +117,7 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, accessTo
 
     const bulkActionButtons = (
         <div className='flex justify-end items-center gap-3'>
-            {processedCount + errorCount > 0 && (
+            {finishedCount > 0 && (
                 <Menu as='div' className='relative inline-block text-left'>
                     <Menu.Button className='border rounded-md p-1 bg-gray-500 text-white px-2'>
                         <BiTrash className='inline-block w-4 h-4 -mt-0.5 mr-1.5' />
@@ -138,7 +143,7 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, accessTo
                                         }
                                     >
                                         <BiTrash className='inline-block w-4 h-4 -mt-0.5 mr-1.5' />
-                                        Discard {errorCount} sequences with errors
+                                        Discard {errorCount} sequence{errorCount > 1 ? 's' : ''} with errors
                                     </button>
                                 </Menu.Item>
                             )}
@@ -147,7 +152,7 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, accessTo
                                     className={menuItemClassName}
                                     onClick={() =>
                                         displayConfirmationDialog({
-                                            dialogText: `Are you sure you want to discard all ${processedCount + errorCount} processed sequences?`,
+                                            dialogText: `Are you sure you want to discard all ${finishedCount} processed sequences?`,
                                             onConfirmation: () => {
                                                 hooks.deleteSequenceEntries({
                                                     scope: deleteAllDataScope.value,
@@ -157,19 +162,19 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, accessTo
                                     }
                                 >
                                     <BiTrash className='inline-block w-4 h-4 -mt-0.5 mr-1.5' />
-                                    Discard all {processedCount + errorCount} processed sequences
+                                    Discard all {finishedCount} processed sequences
                                 </button>
                             </Menu.Item>
                         </div>
                     </Menu.Items>
                 </Menu>
             )}
-            {processedCount > 0 && (
+            {processedCount + revocationCount > 0 && (
                 <button
                     className='border rounded-md p-1 bg-gray-500 text-white px-2'
                     onClick={() =>
                         displayConfirmationDialog({
-                            dialogText: 'Are you sure you want to release all sequences without errors?',
+                            dialogText: 'Are you sure you want to release all valid sequences?',
                             onConfirmation: () =>
                                 hooks.approveProcessedData({
                                     scope: approveAllDataScope.value,
@@ -178,7 +183,8 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, accessTo
                     }
                 >
                     <WpfPaperPlane className='inline-block w-4 h-4 -mt-0.5 mr-1.5' />
-                    Release {processedCount} sequences without errors
+                    Release {processedCount + revocationCount} valid sequence
+                    {processedCount + revocationCount > 1 ? 's' : ''}
                 </button>
             )}
         </div>

website/src/components/SequenceDetailsPage/RevokeButton.tsx

@@ -0,0 +1,49 @@
+import { type FC } from 'react';
+import { toast } from 'react-toastify';
+
+import { routes } from '../../routes';
+import { backendClientHooks } from '../../services/serviceHooks';
+import type { ClientConfig } from '../../types/runtimeConfig';
+import { createAuthorizationHeader } from '../../utils/createAuthorizationHeader';
+import { stringifyMaybeAxiosError } from '../../utils/stringifyMaybeAxiosError';
+import { withQueryProvider } from '../common/withQueryProvider';
+
+type RevokeSequenceEntryProps = {
+    organism: string;
+    accessToken: string;
+    clientConfig: ClientConfig;
+    accessionVersion: string;
+};
+
+const InnerRevokeButton: FC<RevokeSequenceEntryProps> = ({ organism, accessToken, clientConfig, accessionVersion }) => {
+    const hooks = backendClientHooks(clientConfig);
+    const useRevokeSequenceEntries = hooks.useRevokeSequences(
+        { headers: createAuthorizationHeader(accessToken), params: { organism } },
+        {
+            onSuccess: () => {
+                document.location = routes.userSequenceReviewPage(organism);
+            },
+            onError: (error) =>
+                toast.error(getRevokeSequenceEntryErrorMessage(error), {
+                    position: 'top-center',
+                    autoClose: false,
+                }),
+        },
+    );
+
+    const handleRevokeSequenceEntry = () => {
+        useRevokeSequenceEntries.mutate({ accessions: [accessionVersion] });
+    };
+
+    return (
+        <button className='btn btn-sm  bg-red-400' onClick={handleRevokeSequenceEntry}>
+            Revoke this sequence
+        </button>
+    );
+};
+
+export const RevokeButton = withQueryProvider(InnerRevokeButton);
+
+function getRevokeSequenceEntryErrorMessage(error: unknown) {
+    return 'Failed to revoke sequence entry: ' + stringifyMaybeAxiosError(error);
+}