Add changes to work on for later

loculus-project · Jul 30, 2024 · 75e3b07 · 75e3b07
1 parent 409bb64
commit 75e3b07
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Showing 8 changed files with 10 additions and 9 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
@@ -74,7 +74,7 @@ data class AccessionsToRevokeWithComments(
     )
     val accessions: List<Accession>,
     @Schema(
-        description = "Reason for revocation or other details, added as version_comments",
+        description = "Reason for revocation or other details, added as recovation_comments",
     )
     val revocationComments: String? = null,
 )

diff --git a/backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt b/backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt
@@ -57,6 +57,7 @@ class ReleasedDataModel(
         }
 
         var metadata = rawProcessedData.processedData.metadata +
+            ("version_comments" to TextNode(rawProcessedData.revocationComments)) +
             ("accession" to TextNode(rawProcessedData.accession)) +
             ("version" to LongNode(rawProcessedData.version)) +
             (HEADER_TO_CONNECT_METADATA_AND_SEQUENCES to TextNode(rawProcessedData.submissionId)) +

diff --git a/backend/src/main/kotlin/org/loculus/backend/service/submission/MetadataUploadAuxTable.kt b/backend/src/main/kotlin/org/loculus/backend/service/submission/MetadataUploadAuxTable.kt
@@ -9,7 +9,6 @@ const val METADATA_UPLOAD_TABLE_NAME = "metadata_upload_aux_table"
 object MetadataUploadAuxTable : Table(METADATA_UPLOAD_TABLE_NAME) {
     val accessionColumn = varchar("accession", 255).nullable()
     val versionColumn = long("version").nullable()
-    val versionCommentColumn = varchar("version_comment", 255).nullable()
     val uploadIdColumn = varchar("upload_id", 255)
     val organismColumn = varchar("organism", 255)
     val submissionIdColumn = varchar("submission_id", 255)

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
@@ -21,7 +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 revocationCommentsColumn = varchar("revocation_comments", 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 revocationCommentsColumn = varchar("revocation_comments", 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
@@ -578,6 +578,7 @@ class SubmissionDatabaseService(
                     DataUseTermsType.fromString(it[DataUseTermsTable.dataUseTermsTypeColumn]),
                     it[DataUseTermsTable.restrictedUntilColumn],
                 ),
+                revocationComments = it[SequenceEntriesView.revocationCommentsColumn],
             )
         }
 
@@ -674,7 +675,7 @@ class SubmissionDatabaseService(
         accessions: List<Accession>,
         authenticatedUser: AuthenticatedUser,
         organism: Organism,
-        revocationComment: String?,
+        revocationComments: String?,
     ): List<SubmissionIdMapping> {
         log.info { "revoking ${accessions.size} sequences" }
 
@@ -686,7 +687,7 @@ class SubmissionDatabaseService(
         }
 
         val now = Clock.System.now().toLocalDateTime(TimeZone.UTC)
-        val comment = revocationComment ?: ""
+        val comment = revocationComments ?: ""
         SequenceEntriesTable.insert(
             SequenceEntriesTable
                 .select(
@@ -707,7 +708,7 @@ class SubmissionDatabaseService(
             columns = listOf(
                 SequenceEntriesTable.accessionColumn,
                 SequenceEntriesTable.versionColumn,
-                SequenceEntriesTable.versionCommentColumn,
+                SequenceEntriesTable.revocationCommentsColumn,
                 SequenceEntriesTable.submissionIdColumn,
                 SequenceEntriesTable.submitterColumn,
                 SequenceEntriesTable.groupIdColumn,
@@ -1022,6 +1023,7 @@ data class RawProcessedData(
     override val accession: Accession,
     override val version: Version,
     val isRevocation: Boolean,
+    val revocationComments: String?,
     val submitter: String,
     val groupId: Int,
     val groupName: String,

diff --git a/backend/src/main/kotlin/org/loculus/backend/service/submission/UploadDatabaseService.kt b/backend/src/main/kotlin/org/loculus/backend/service/submission/UploadDatabaseService.kt
@@ -29,7 +29,6 @@ import org.loculus.backend.service.submission.MetadataUploadAuxTable.submissionI
 import org.loculus.backend.service.submission.MetadataUploadAuxTable.submitterColumn
 import org.loculus.backend.service.submission.MetadataUploadAuxTable.uploadIdColumn
 import org.loculus.backend.service.submission.MetadataUploadAuxTable.uploadedAtColumn
-import org.loculus.backend.service.submission.MetadataUploadAuxTable.versionCommentColumn
 import org.loculus.backend.service.submission.SequenceUploadAuxTable.compressedSequenceDataColumn
 import org.loculus.backend.service.submission.SequenceUploadAuxTable.segmentNameColumn
 import org.loculus.backend.service.submission.SequenceUploadAuxTable.sequenceSubmissionIdColumn
@@ -64,7 +63,6 @@ class UploadDatabaseService(
         uploadedAt: LocalDateTime,
     ) {
         MetadataUploadAuxTable.batchInsert(uploadedMetadataBatch) {
-            this[versionCommentColumn] = it.metadata["version_comment"]
             this[submitterColumn] = authenticatedUser.username
             this[groupIdColumn] = groupId
             this[uploadedAtColumn] = uploadedAt
@@ -84,7 +82,6 @@ class UploadDatabaseService(
     ) {
         MetadataUploadAuxTable.batchInsert(uploadedRevisedMetadataBatch) {
             this[accessionColumn] = it.accession
-            this[versionCommentColumn] = it.metadata["version_comment"]
             this[submitterColumn] = authenticatedUser.username
             this[uploadedAtColumn] = uploadedAt
             this[submissionIdColumn] = it.submissionId

diff --git a/backend/src/main/resources/db/migration/V1__init.sql b/backend/src/main/resources/db/migration/V1__init.sql
@@ -33,6 +33,7 @@ create table sequence_entries (
     submitted_at timestamp not null,
     released_at timestamp,
     is_revocation boolean not null default false,
+    revocation_comment text,
     original_data jsonb,
     primary key (accession, version),
     foreign key (group_id) references groups_table(group_id)