refactor getSequences usage in SeqSetCitationsController (#3193)

Co-authored-by: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com>
loculus-project · Nov 11, 2024 · 284fed3 · 284fed3
1 parent 93f9902
commit 284fed3
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Showing 4 changed files with 34 additions and 38 deletions.
diff --git a/backend/src/main/kotlin/org/loculus/backend/controller/SeqSetCitationsController.kt b/backend/src/main/kotlin/org/loculus/backend/controller/SeqSetCitationsController.kt
@@ -7,7 +7,6 @@ import org.loculus.backend.api.CitedBy
 import org.loculus.backend.api.ResponseSeqSet
 import org.loculus.backend.api.SeqSet
 import org.loculus.backend.api.SeqSetRecord
-import org.loculus.backend.api.Status.APPROVED_FOR_RELEASE
 import org.loculus.backend.api.SubmittedSeqSet
 import org.loculus.backend.api.SubmittedSeqSetRecord
 import org.loculus.backend.api.SubmittedSeqSetUpdate
@@ -92,11 +91,10 @@ class SeqSetCitationsController(
 
     @Operation(description = "Get count of user sequences cited by SeqSets")
     @GetMapping("/get-user-cited-by-seqset")
-    fun getUserCitedBySeqSet(@HiddenParam authenticatedUser: AuthenticatedUser): CitedBy {
-        val statusFilter = listOf(APPROVED_FOR_RELEASE)
-        val userSequences = submissionDatabaseService.getSequences(authenticatedUser, null, null, statusFilter)
-        return seqSetCitationsService.getUserCitedBySeqSet(userSequences.sequenceEntries)
-    }
+    fun getUserCitedBySeqSet(@HiddenParam authenticatedUser: AuthenticatedUser): CitedBy =
+        seqSetCitationsService.getUserCitedBySeqSet(
+            submissionDatabaseService.getApprovedUserAccessionVersions(authenticatedUser),
+        )
 
     @Operation(description = "Get count of SeqSet cited by publications")
     @GetMapping("/get-seqset-cited-by-publication")

diff --git a/...main/kotlin/org/loculus/backend/service/seqsetcitations/SeqSetCitationsDatabaseService.kt b/...main/kotlin/org/loculus/backend/service/seqsetcitations/SeqSetCitationsDatabaseService.kt
@@ -24,7 +24,6 @@ import org.loculus.backend.api.ResponseSeqSet
 import org.loculus.backend.api.SeqSet
 import org.loculus.backend.api.SeqSetCitationsConstants
 import org.loculus.backend.api.SeqSetRecord
-import org.loculus.backend.api.SequenceEntryStatus
 import org.loculus.backend.api.Status.APPROVED_FOR_RELEASE
 import org.loculus.backend.api.SubmittedSeqSetRecord
 import org.loculus.backend.auth.AuthenticatedUser
@@ -367,7 +366,7 @@ class SeqSetCitationsDatabaseService(
         )
     }
 
-    fun getUserCitedBySeqSet(userAccessions: List<SequenceEntryStatus>): CitedBy {
+    fun getUserCitedBySeqSet(accessionVersions: List<AccessionVersion>): CitedBy {
         log.info { "Get user cited by seqSet" }
 
         data class SeqSetWithAccession(
@@ -377,9 +376,9 @@ class SeqSetCitationsDatabaseService(
             val createdAt: Timestamp,
         )
 
-        val userAccessionStrings = userAccessions.flatMap {
-            listOf(it.accession.plus('.').plus(it.version), it.accession)
-        }
+        val userAccessionStrings = accessionVersions
+            .flatMap { listOf(it.accession, it.displayAccessionVersion()) }
+            .toSet()
 
         val maxSeqSetVersion = SeqSetsTable.seqSetVersion.max().alias("max_version")
         val maxVersionPerSeqSet = SeqSetsTable

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
@@ -52,6 +52,7 @@ import org.loculus.backend.api.ProcessedData
 import org.loculus.backend.api.SequenceEntryStatus
 import org.loculus.backend.api.SequenceEntryVersionToEdit
 import org.loculus.backend.api.Status
+import org.loculus.backend.api.Status.APPROVED_FOR_RELEASE
 import org.loculus.backend.api.SubmissionIdMapping
 import org.loculus.backend.api.SubmittedProcessedData
 import org.loculus.backend.api.UnprocessedData
@@ -623,7 +624,7 @@ open class SubmissionDatabaseService(
 
     fun getSequences(
         authenticatedUser: AuthenticatedUser,
-        organism: Organism?,
+        organism: Organism,
         groupIdsFilter: List<Int>?,
         statusesFilter: List<Status>?,
         warningsFilter: WarningsFilter? = null,
@@ -663,12 +664,9 @@ open class SubmissionDatabaseService(
                 DataUseTermsTable.restrictedUntilColumn,
             )
             .where { groupCondition }
+            .andWhere { SequenceEntriesView.organismIs(organism) }
             .orderBy(SequenceEntriesView.accessionColumn)
 
-        if (organism != null) {
-            baseQuery.andWhere { SequenceEntriesView.organismIs(organism) }
-        }
-
         val statusCounts: Map<Status, Int> = Status.entries.associateWith { status ->
             baseQuery.count { it[SequenceEntriesView.statusColumn] == status.name }
         }
@@ -950,6 +948,24 @@ open class SubmissionDatabaseService(
         )
     }
 
+    /**
+     * Returns AccessionVersions submitted by groups that the given user is part of
+     * and that are approved for release.
+     */
+    fun getApprovedUserAccessionVersions(authenticatedUser: AuthenticatedUser): List<AccessionVersion> =
+        SequenceEntriesView.select(
+            SequenceEntriesView.accessionColumn,
+            SequenceEntriesView.versionColumn,
+        )
+            .where(SequenceEntriesView.statusIs(APPROVED_FOR_RELEASE))
+            .groupBy(getGroupCondition(null, authenticatedUser))
+            .map {
+                AccessionVersion(
+                    it[SequenceEntriesView.accessionColumn],
+                    it[SequenceEntriesView.versionColumn],
+                )
+            }
+
     private fun originalMetadataFilter(
         authenticatedUser: AuthenticatedUser,
         organism: Organism,

diff --git a/...d/src/test/kotlin/org/loculus/backend/controller/seqsetcitations/CitationEndpointsTest.kt b/...d/src/test/kotlin/org/loculus/backend/controller/seqsetcitations/CitationEndpointsTest.kt
@@ -7,10 +7,7 @@ import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.params.ParameterizedTest
 import org.junit.jupiter.params.provider.MethodSource
-import org.loculus.backend.api.DataUseTerms
-import org.loculus.backend.api.GetSequenceResponse
-import org.loculus.backend.api.SequenceEntryStatus
-import org.loculus.backend.api.Status
+import org.loculus.backend.api.AccessionVersion
 import org.loculus.backend.controller.EndpointTest
 import org.loculus.backend.controller.expectUnauthorizedResponse
 import org.loculus.backend.service.submission.AccessionPreconditionValidator
@@ -46,8 +43,8 @@ class CitationEndpointsTest(@Autowired private val client: SeqSetCitationsContro
     @Test
     fun `WHEN calling get user cited by seqSet of non-existing user THEN returns empty results`() {
         every {
-            submissionDatabaseService.getSequences(any(), any(), any(), any())
-        } returns GetSequenceResponse(sequenceEntries = emptyList(), statusCounts = emptyMap())
+            submissionDatabaseService.getApprovedUserAccessionVersions(any())
+        } returns listOf()
 
         client.getUserCitedBySeqSet()
             .andExpect(status().isOk)
@@ -72,22 +69,8 @@ class CitationEndpointsTest(@Autowired private val client: SeqSetCitationsContro
     @Test
     fun `WHEN calling get seqSet cited by publication of existing seqSet THEN returns results`() {
         every {
-            submissionDatabaseService.getSequences(any(), any(), any(), any())
-        } returns GetSequenceResponse(
-            sequenceEntries = listOf(
-                SequenceEntryStatus(
-                    accession = "mock-sequence-accession",
-                    version = 1L,
-                    status = Status.APPROVED_FOR_RELEASE,
-                    groupId = 123,
-                    submitter = "mock-submitter",
-                    isRevocation = false,
-                    submissionId = "mock-submission-id",
-                    dataUseTerms = DataUseTerms.Open,
-                ),
-            ),
-            statusCounts = mapOf(Status.APPROVED_FOR_RELEASE to 1),
-        )
+            submissionDatabaseService.getApprovedUserAccessionVersions(any())
+        } returns listOf(AccessionVersion("mock-sequence-accession", 1L))
 
         val seqSetResult = client.createSeqSet()
             .andExpect(status().isOk)