Reviewpage redesign (#1373)

loculus-project · Mar 22, 2024 · b1639c2 · b1639c2
1 parent 0e68d98
commit b1639c2
Show file tree

Hide file tree

Showing 9 changed files with 31 additions and 11 deletions.
diff --git a/backend/src/main/kotlin/org/loculus/backend/controller/DatasetCitationsController.kt b/backend/src/main/kotlin/org/loculus/backend/controller/DatasetCitationsController.kt
@@ -97,7 +97,7 @@ class DatasetCitationsController(
     @GetMapping("/get-user-cited-by-dataset")
     fun getUserCitedByDataset(@UsernameFromJwt username: String): CitedBy {
         val statusFilter = listOf(APPROVED_FOR_RELEASE)
-        val userSequences = submissionDatabaseService.getSequences(username, null, null, statusFilter)
+        val userSequences = submissionDatabaseService.getSequences(username, null, null, statusFilter, statusFilter)
         return datasetCitationsService.getUserCitedByDataset(userSequences.sequenceEntries)
     }
 

diff --git a/backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt b/backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt
@@ -255,6 +255,8 @@ class SubmissionController(
         )
         @RequestParam(required = false)
         statusesFilter: List<Status>?,
+        @RequestParam(required = false)
+        initialStatusesFilter: List<Status>?,
         @UsernameFromJwt username: String,
         @RequestParam(required = false, defaultValue = "INCLUDE_WARNINGS")
         warningsFilter: WarningsFilter,
@@ -275,6 +277,7 @@ class SubmissionController(
         organism,
         groupsFilter,
         statusesFilter,
+        initialStatusesFilter,
         warningsFilter,
         page,
         size,

diff --git a/backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt b/backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt
@@ -414,6 +414,7 @@ class SubmissionDatabaseService(
         organism: Organism?,
         groupsFilter: List<String>?,
         statusesFilter: List<Status>?,
+        statusesInitialFilter: List<Status>?,
         warningsFilter: WarningsFilter? = null,
         page: Int? = null,
         size: Int? = null,
@@ -431,6 +432,7 @@ class SubmissionDatabaseService(
         }
 
         val listOfStatuses = statusesFilter ?: Status.entries
+        val listOfInitialStatuses = statusesInitialFilter ?: Status.entries
 
         sequenceEntriesTableProvider.get(organism).let { table ->
             val baseQuery = table
@@ -456,7 +458,8 @@ class SubmissionDatabaseService(
                 )
                 .select(
                     where = {
-                        table.groupNameIsOneOf(validatedGroupNames)
+                        table.statusIsOneOf(listOfInitialStatuses) and
+                            table.groupNameIsOneOf(validatedGroupNames)
                     },
                 )
                 .orderBy(table.accessionColumn)

diff --git a/.../src/test/kotlin/org/loculus/backend/controller/datasetcitations/CitationEndpointsTest.kt b/.../src/test/kotlin/org/loculus/backend/controller/datasetcitations/CitationEndpointsTest.kt
@@ -62,7 +62,7 @@ class CitationEndpointsTest(
     @Test
     fun `WHEN calling get user cited by dataset of non-existing user THEN returns empty results`() {
         every {
-            submissionDatabaseService.getSequences(any(), any(), any(), any())
+            submissionDatabaseService.getSequences(any(), any(), any(), any(), any())
         } returns GetSequenceResponse(sequenceEntries = emptyList(), statusCounts = emptyMap())
 
         client.getUserCitedByDataset()
@@ -88,7 +88,7 @@ class CitationEndpointsTest(
     @Test
     fun `WHEN calling get dataset cited by publication of existing dataset THEN returns results`() {
         every {
-            submissionDatabaseService.getSequences(any(), any(), any(), any())
+            submissionDatabaseService.getSequences(any(), any(), any(), any(), any())
         } returns GetSequenceResponse(
             sequenceEntries = listOf(
                 SequenceEntryStatus(

diff --git a/...d/src/test/kotlin/org/loculus/backend/controller/submission/SubmissionControllerClient.kt b/...d/src/test/kotlin/org/loculus/backend/controller/submission/SubmissionControllerClient.kt
@@ -86,6 +86,7 @@ class SubmissionControllerClient(private val mockMvc: MockMvc, private val objec
         organism: String = DEFAULT_ORGANISM,
         groupsFilter: List<String>? = null,
         statusesFilter: List<Status>? = null,
+        initialStatusesFilter: List<Status>? = null,
         warningsFilter: WarningsFilter? = null,
         jwt: String? = jwtForDefaultUser,
         page: Int? = null,
@@ -96,6 +97,7 @@ class SubmissionControllerClient(private val mockMvc: MockMvc, private val objec
                 .withAuth(jwt)
                 .param("groupsFilter", groupsFilter?.joinToString { it })
                 .param("statusesFilter", statusesFilter?.joinToString { it.name })
+                .param("initialStatusesFilter", initialStatusesFilter?.joinToString { it.name })
                 .param("warningsFilter", warningsFilter?.name)
                 .param("page", page?.toString())
                 .param("size", size?.toString()),

diff --git a/.../src/test/kotlin/org/loculus/backend/controller/submission/SubmissionConvenienceClient.kt b/.../src/test/kotlin/org/loculus/backend/controller/submission/SubmissionConvenienceClient.kt
@@ -161,6 +161,7 @@ class SubmissionConvenienceClient(
         username: String = DEFAULT_USER_NAME,
         groupsFilter: List<String>? = null,
         statusesFilter: List<Status>? = null,
+        initialStatusesFilter: List<Status>? = null,
         organism: String = DEFAULT_ORGANISM,
         warningsFilter: WarningsFilter = WarningsFilter.INCLUDE_WARNINGS,
         page: Int? = null,
@@ -170,6 +171,7 @@ class SubmissionConvenienceClient(
             organism = organism,
             groupsFilter = groupsFilter,
             statusesFilter = statusesFilter,
+            initialStatusesFilter = initialStatusesFilter,
             warningsFilter = warningsFilter,
             jwt = generateJwtFor(username),
             page = page,

diff --git a/website/src/components/ReviewPage/ReviewCard.tsx b/website/src/components/ReviewPage/ReviewCard.tsx
@@ -51,7 +51,7 @@ export const ReviewCard: FC<ReviewCardProps> = ({
     const { isLoading, data } = useGetMetadataAndAnnotations(organism, clientConfig, accessToken, sequenceEntryStatus);
 
     return (
-        <div className='p-3 border rounded-md shadow-lg relative transition-all duration-500'>
+        <div className='px-3 py-2   relative transition-all duration-500'>
             <div className='flex'>
                 <div className='flex flex-grow flex-wrap '>
                     <StatusIcon

diff --git a/website/src/components/ReviewPage/ReviewPage.tsx b/website/src/components/ReviewPage/ReviewPage.tsx
@@ -287,7 +287,7 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, accessTo
     );
 
     const reviewCards = (
-        <div className='flex flex-col gap-2 py-4'>
+        <div className='flex flex-col gap-2 py-4 divide-y divide-gray-200'>
             {sequences.map((sequence) => {
                 return (
                     <div key={sequence.accession}>
@@ -322,9 +322,17 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, accessTo
         <>
             <ManagedErrorFeedback message={errorMessage} open={isErrorOpen} onClose={closeErrorFeedback} />
             <div className={hooks.getSequences.isLoading ? 'opacity-50 pointer-events-none' : ''}>
-                <div className='flex sm:justify-between items-bottom flex-col md:flex-row gap-5'>
-                    {controlPanel}
-                    {bulkActionButtons}
+                <div className='sticky top-0 z-10'>
+                    <div className='flex sm:justify-between items-bottom flex-col md:flex-row gap-5 bg-white pb-1'>
+                        {controlPanel}
+                        {bulkActionButtons}
+                    </div>
+                    <div
+                        className='h-2 w-full'
+                        style={{
+                            background: 'linear-gradient(0deg, rgba(255, 255, 255, 0) 0%,rgba(100, 100, 100, .2) 80%)',
+                        }}
+                    ></div>
                 </div>
                 {reviewCards}
                 {pagination}

diff --git a/website/src/hooks/useSubmissionOperations.ts b/website/src/hooks/useSubmissionOperations.ts
@@ -24,20 +24,22 @@ export function useSubmissionOperations(
     pageQuery: PageQuery,
 ) {
     const hooks = useMemo(() => backendClientHooks(clientConfig), [clientConfig]);
-    const [includedStatuses, setIncludedStatuses] = useState<string[]>([
+    const allRelevantStatuses = [
         receivedStatus,
         inProcessingStatus,
         hasErrorsStatus,
         awaitingApprovalStatus,
         awaitingApprovalForRevocationStatus,
-    ]);
+    ];
+    const [includedStatuses, setIncludedStatuses] = useState<string[]>(allRelevantStatuses);
     const useGetSequences = hooks.useGetSequences(
         {
             headers: createAuthorizationHeader(accessToken),
             params: {
                 organism,
             },
             queries: {
+                initialStatusesFilter: allRelevantStatuses.join(','),
                 statusesFilter: includedStatuses.join(','),
                 page: pageQuery.page - 1,
                 size: pageQuery.size,