feat(backend): fix merge conflicts

Author: anna-parker

backend/src/main/kotlin/org/loculus/backend/config/ReferenceGenome.kt

@@ -15,8 +15,6 @@ data class ReferenceGenome(val nucleotideSequences: List<ReferenceSequence>, val
         return "ReferenceGenome(nucleotideSequences=[$nucleotideSequencesString], genes=[$genesString])"
     }
 
-    fun allSegmentsConcatenated(): String = nucleotideSequences.joinToString(separator = "") { it.sequence }
-
     fun getNucleotideSegmentReference(segmentName: String): GeneticSequence? = nucleotideSequences
         .find { it.name == segmentName }
         ?.sequence

backend/src/main/kotlin/org/loculus/backend/service/submission/CompressionService.kt

@@ -44,6 +44,7 @@ class CompressionService(
 
     private fun decompressNucleotideSequence(
         compressedSequence: CompressedSequence,
+        segmentName: String,
         organism: Organism,
     ): GeneticSequence = decompress(
         compressedSequence,
@@ -75,7 +76,7 @@ class CompressionService(
                 .unalignedNucleotideSequences.mapValues {
                     when (val compressedSequence = it.value) {
                         null -> null
-                        else -> decompressNucleotideSequence(compressedSequence, organism)
+                        else -> decompressNucleotideSequence(compressedSequence, it.key, organism)
                     }
                 },
             originalData.files,
@@ -100,13 +101,13 @@ class CompressionService(
                 .unalignedNucleotideSequences.mapValues { (segmentName, sequenceData) ->
                     when (sequenceData) {
                         null -> null
-                        else -> decompressNucleotideSequence(sequenceData, organism)
+                        else -> decompressNucleotideSequence(sequenceData, segmentName, organism)
                     }
                 },
             processedData.alignedNucleotideSequences.mapValues { (segmentName, sequenceData) ->
                 when (sequenceData) {
                     null -> null
-                    else -> decompressNucleotideSequence(sequenceData, organism)
+                    else -> decompressNucleotideSequence(sequenceData, segmentName, organism)
                 }
             },
             processedData.nucleotideInsertions,
@@ -126,13 +127,13 @@ class CompressionService(
             .unalignedNucleotideSequences.mapValues { (segmentName, sequenceData) ->
                 when (sequenceData) {
                     null -> null
-                    else -> compressNucleotideSequence(sequenceData, organism)
+                    else -> compressNucleotideSequence(sequenceData, segmentName, organism)
                 }
             },
         processedData.alignedNucleotideSequences.mapValues { (segmentName, sequenceData) ->
             when (sequenceData) {
                 null -> null
-                else -> compressNucleotideSequence(sequenceData, organism)
+                else -> compressNucleotideSequence(sequenceData, segmentName, organism)
             }
         },
         processedData.nucleotideInsertions,
@@ -191,10 +192,14 @@ class CompressionService(
         return String(decompressedBuffer, 0, decompressionReturnCode.toInt(), StandardCharsets.UTF_8)
     }
 
-    private fun getDictionaryForNucleotideSequences(organism: Organism): ByteArray? = backendConfig
-        .getInstanceConfig(organism)
-        .referenceGenome.allSegmentsConcatenated()
-        ?.toByteArray()
+    private fun getDictionaryForNucleotideSequenceSegment(segmentName: String, organism: Organism): ByteArray? =
+        backendConfig
+            .getInstanceConfig(organism)
+            .referenceGenome
+            .getNucleotideSegmentReference(
+                segmentName,
+            )
+            ?.toByteArray()
 
     private fun getDictionaryForAminoAcidSequence(geneName: String, organism: Organism): ByteArray? = backendConfig
         .getInstanceConfig(organism)

…migration/V1.18__refactor_aux_tables.sql …migration/V1.19__refactor_aux_tables.sqlbackend/src/main/resources/db/migration/V1.18__refactor_aux_tables.sql renamed to backend/src/main/resources/db/migration/V1.19__refactor_aux_tables.sql backend/src/main/resources/db/migration/V1.18__refactor_aux_tables.sql renamed to backend/src/main/resources/db/migration/V1.19__refactor_aux_tables.sql

@@ -100,6 +100,12 @@ object SubmitFiles {
         val submissionIds = List(10) { "custom$it" }
 
         const val NUMBER_OF_SEQUENCES = 10
+
+        private fun getFileContent(file: String): String = String(
+            this::class.java.classLoader.getResourceAsStream(file)?.readBytes() ?: error(
+                "$file resource for tests not found",
+            ),
+        )
     }
 
     fun metadataFileWith(