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loculus-project · Nov 8, 2024 · afc657f · afc657f
1 parent 1b1dcb0
commit afc657f
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Showing 4 changed files with 36 additions and 12 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
@@ -219,6 +219,15 @@ data class SequenceEntryStatus(
     val isRevocation: Boolean = false,
     val submissionId: String,
     val dataUseTerms: DataUseTerms,
+    val processedData: ProcessedData<GeneticSequence>,
+    val originalData: OriginalData<GeneticSequence>,
+    @Schema(description = "The preprocessing will be considered failed if this is not empty")
+    val errors: List<PreprocessingAnnotation>? = null,
+    @Schema(
+        description =
+        "Issues where data is not necessarily wrong, but the user might want to look into those warnings.",
+    )
+    val warnings: List<PreprocessingAnnotation>? = null,
 ) : AccessionVersionInterface
 
 data class EditedSequenceEntryData(

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
@@ -707,6 +707,16 @@ class SubmissionDatabaseService(
                         DataUseTermsType.fromString(row[DataUseTermsTable.dataUseTermsTypeColumn]),
                         row[DataUseTermsTable.restrictedUntilColumn],
                     ),
+                    processedData = compressionService.decompressSequencesInProcessedData(
+                        row[SequenceEntriesView.processedDataColumn]!!,
+                        organism!!,
+                    ),
+                    originalData = compressionService.decompressSequencesInOriginalData(
+                        row[SequenceEntriesView.originalDataColumn]!!,
+                        organism!!,
+                    ),
+                    errors = row[SequenceEntriesView.errorsColumn],
+                    warnings = row[SequenceEntriesView.warningsColumn],
                 )
             }
 

diff --git a/website/src/components/ReviewPage/ReviewCard.tsx b/website/src/components/ReviewPage/ReviewCard.tsx
@@ -167,6 +167,7 @@ const isAnnotationPresent = (metadataField: string) => (item: ProcessingAnnotati
     item.source[0].name === metadataField;
 
 const MetadataList: FC<MetadataListProps> = ({ data }) =>
+    data.processedData !== undefined &&
     Object.entries(data.processedData.metadata).map(([metadataName, value], index) =>
         value === null ? null : (
             <KeyValueComponent

diff --git a/website/src/types/backend.ts b/website/src/types/backend.ts
@@ -135,18 +135,22 @@ export const sequenceEntryStatus = accessionVersion.merge(
         submitter: z.string(),
         errors: z.array(processingAnnotation).nullable(),
         warnings: z.array(processingAnnotation).nullable(),
-        originalData: z.object({
-            metadata: unprocessedMetadataRecord,
-            unalignedNucleotideSequences: z.record(z.string()),
-        }),
-        processedData: z.object({
-            metadata: metadataRecord,
-            unalignedNucleotideSequences: z.record(z.string().nullable()),
-            alignedNucleotideSequences: z.record(z.string().nullable()),
-            nucleotideInsertions: z.record(z.array(z.string())),
-            alignedAminoAcidSequences: z.record(z.string().nullable()),
-            aminoAcidInsertions: z.record(z.array(z.string())),
-        }),
+        originalData: z
+            .object({
+                metadata: unprocessedMetadataRecord,
+                unalignedNucleotideSequences: z.record(z.string()),
+            })
+            .optional(),
+        processedData: z
+            .object({
+                metadata: metadataRecord,
+                unalignedNucleotideSequences: z.record(z.string().nullable()),
+                alignedNucleotideSequences: z.record(z.string().nullable()),
+                nucleotideInsertions: z.record(z.array(z.string())),
+                alignedAminoAcidSequences: z.record(z.string().nullable()),
+                aminoAcidInsertions: z.record(z.array(z.string())),
+            })
+            .optional(),
     }),
 );