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

… well. (#2352) * Rename version_comment metadata field versionComment for internal consistency. * Add a versionComment field to the revoke endpoint, make sure versionComment is added to get-released-data output. * Add DB schema updates as new flyway version. * Add revocation comment to backend tests * Add comment option to revoke button * Add version comments to revocationentrydatatable and not just preview.
loculus-project · Aug 19, 2024 · a9fa920 · a9fa920
1 parent d168fe0
commit a9fa920
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Showing 17 changed files with 206 additions and 41 deletions.
diff --git a/backend/src/main/kotlin/org/loculus/backend/api/SubmissionTypes.kt b/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",
+    )
+    val versionComment: String? = null,
+)
+
 enum class ApproveDataScope {
     ALL,
     WITHOUT_WARNINGS,

diff --git a/backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt b/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)

diff --git a/backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt b/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) +
+            ("versionComment" to TextNode(rawProcessedData.versionComment))
 
         if (backendConfig.dataUseTermsUrls != null) {
             val url = if (rawProcessedData.dataUseTerms == DataUseTerms.Open) {

diff --git a/backend/src/main/kotlin/org/loculus/backend/service/submission/SequenceEntriesTable.kt b/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)

diff --git a/backend/src/main/kotlin/org/loculus/backend/service/submission/SequenceEntriesView.kt b/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()
 

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
@@ -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,

diff --git a/backend/src/main/resources/db/migration/V1.1__add_field.sql b/backend/src/main/resources/db/migration/V1.1__add_field.sql
@@ -0,0 +1,30 @@
+alter table sequence_entries add column version_comment text;
+
+drop view if exists  sequence_entries_view;
+
+create view sequence_entries_view as
+select
+    se.*,
+    sepd.started_processing_at,
+    sepd.finished_processing_at,
+    sepd.processed_data as processed_data,
+    sepd.processed_data || em.joint_metadata as joint_metadata,
+    sepd.errors,
+    sepd.warnings,
+    case
+        when se.released_at is not null then 'APPROVED_FOR_RELEASE'
+        when se.is_revocation then 'AWAITING_APPROVAL'
+        when sepd.processing_status = 'IN_PROCESSING' then 'IN_PROCESSING'
+        when sepd.processing_status = 'HAS_ERRORS' then 'HAS_ERRORS'
+        when sepd.processing_status = 'FINISHED' then 'AWAITING_APPROVAL'
+        else 'RECEIVED'
+    end as status
+from
+    sequence_entries se
+    left join sequence_entries_preprocessed_data sepd on
+        se.accession = sepd.accession
+        and se.version = sepd.version
+        and sepd.pipeline_version = (select version from current_processing_pipeline)
+    left join external_metadata_view em on
+        se.accession = em.accession
+        and se.version = em.version;
diff --git a/.../src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt b/.../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(),
+                "versionComment" 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())),
                 )
+
+                "versionComment" -> assertThat(
+                    value,
+                    `is`(TextNode("This is a test revocation")),
+                )
+
                 else -> assertThat("value for $key", value, `is`(NullNode.instance))
             }
         }

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
@@ -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":${objectMapper.writeValueAsString(versionComment)}}""",
+            )
             .withAuth(jwt),
     )
 

diff --git a/.../src/test/kotlin/org/loculus/backend/controller/submission/SubmissionConvenienceClient.kt b/.../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,
         ),
     )
 

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -1007,7 +1007,7 @@ defaultOrganismConfig: &defaultOrganismConfig
         rangeSearch: true
         preprocessing:
           inputs: {input: nextclade.coverage}
-      - name: version_comment
+      - name: versionComment
         displayName: Version Comment
         header: Submission details
     website: &website

diff --git a/website/src/components/SequenceDetailsPage/RevocationEntryDataTable.astro b/website/src/components/SequenceDetailsPage/RevocationEntryDataTable.astro
@@ -8,6 +8,7 @@ import {
     RELEASED_AT_FIELD,
     IS_REVOCATION_FIELD,
     ACCESSION_FIELD,
+    VERSION_COMMENT_FIELD,
     VERSION_STATUS_FIELD,
     SUBMITTER_FIELD,
     GROUP_NAME_FIELD,
@@ -31,6 +32,7 @@ const relevantFieldsForRevocationVersions = [
     ACCESSION_FIELD,
     IS_REVOCATION_FIELD,
     RELEASED_AT_FIELD,
+    VERSION_COMMENT_FIELD,
     VERSION_STATUS_FIELD,
     SUBMITTED_AT_FIELD,
     SUBMITTER_FIELD,