fix(backend): allow segments / genes to be null #822

loculus-project · Jan 24, 2024 · 5ef6d0c · 5ef6d0c
1 parent 4e7c662
commit 5ef6d0c
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Showing 8 changed files with 127 additions and 134 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
@@ -166,7 +166,7 @@ data class OriginalData(
         example = "{\"segment1\": \"ACTG\", \"segment2\": \"GTCA\"}",
         description = "The key is the segment name, the value is the nucleotide sequence",
     )
-    val unalignedNucleotideSequences: Map<SegmentName, NucleotideSequence>,
+    val unalignedNucleotideSequences: Map<SegmentName, NucleotideSequence?>,
 )
 
 enum class Status {

diff --git a/backend/src/main/kotlin/org/loculus/backend/config/ReferenceGenome.kt b/backend/src/main/kotlin/org/loculus/backend/config/ReferenceGenome.kt
@@ -19,20 +19,17 @@ data class ReferenceGenome(
         return "ReferenceGenome(nucleotideSequences=[$nucleotideSequencesString], genes=[$genesString])"
     }
 
-    fun getNucleotideSegmentReference(segmentName: String): NucleotideSequence? = nucleotideSequences.find {
-        it.name == segmentName
-    }?.sequence
-
-    fun getAminoAcidGeneReference(gene: String): AminoAcidSequence? = genes.find {
-        it.name == gene
-    }?.sequence
-
-    private fun shortenSequence(sequence: String): String {
-        return if (sequence.length > 10) {
-            sequence.substring(0, 10) + "..."
-        } else {
-            sequence
-        }
+    fun getNucleotideSegmentReference(segmentName: String): NucleotideSequence? = nucleotideSequences
+        .find { it.name == segmentName }
+        ?.sequence
+
+    fun getAminoAcidGeneReference(gene: String): AminoAcidSequence? = genes
+        .find { it.name == gene }
+        ?.sequence
+
+    private fun shortenSequence(sequence: String) = when {
+        sequence.length > 10 -> sequence.substring(0, 10) + "..."
+        else -> sequence
     }
 
     private fun referenceListToString(list: List<ReferenceSequence>) = list.joinToString(", ") {

diff --git a/backend/src/main/kotlin/org/loculus/backend/service/submission/CompressionService.kt b/backend/src/main/kotlin/org/loculus/backend/service/submission/CompressionService.kt
@@ -53,23 +53,21 @@ class CompressionService(private val backendConfig: BackendConfig) {
         originalData.metadata,
         originalData
             .unalignedNucleotideSequences.mapValues {
-                decompressNucleotideSequence(
-                    it.value,
-                    it.key,
-                    organism,
-                )
+                when (val compressedSequence = it.value) {
+                    null -> null
+                    else -> decompressNucleotideSequence(compressedSequence, it.key, organism)
+                }
             },
     )
 
     fun compressSequencesInOriginalData(originalData: OriginalData, organism: Organism) = OriginalData(
         originalData.metadata,
         originalData
             .unalignedNucleotideSequences.mapValues { (segmentName, sequenceData) ->
-                compressNucleotideSequence(
-                    sequenceData,
-                    segmentName,
-                    organism,
-                )
+                when (sequenceData) {
+                    null -> null
+                    else -> compressNucleotideSequence(sequenceData, segmentName, organism)
+                }
             },
     )
 
@@ -165,12 +163,14 @@ class CompressionService(private val backendConfig: BackendConfig) {
             .referenceGenomes
             .getNucleotideSegmentReference(
                 segmentName,
-            )?.toByteArray()
+            )
+            ?.toByteArray()
 
     private fun getDictionaryForAminoAcidSequence(geneName: String, organism: Organism): ByteArray? = backendConfig
         .getInstanceConfig(organism)
         .referenceGenomes
         .getAminoAcidGeneReference(
             geneName,
-        )?.toByteArray()
+        )
+        ?.toByteArray()
 }
diff --git a/...src/main/kotlin/org/loculus/backend/service/submission/ProcessedSequenceEntryValidator.kt b/...src/main/kotlin/org/loculus/backend/service/submission/ProcessedSequenceEntryValidator.kt
@@ -2,8 +2,10 @@ package org.loculus.backend.service.submission
 
 import com.fasterxml.jackson.databind.JsonNode
 import com.fasterxml.jackson.databind.node.NullNode
+import org.loculus.backend.api.AminoAcidSequence
 import org.loculus.backend.api.Insertion
 import org.loculus.backend.api.MetadataMap
+import org.loculus.backend.api.NucleotideSequence
 import org.loculus.backend.api.Organism
 import org.loculus.backend.api.ProcessedData
 import org.loculus.backend.config.BackendConfig
@@ -245,11 +247,7 @@ class ProcessedSequenceEntryValidator(
         )
     }
 
-    private fun <T> validateNoMissingSegment(
-        segment: ReferenceSequence,
-        sequenceData: Map<String, T>,
-        sequence: String,
-    ) {
+    private fun validateNoMissingSegment(segment: ReferenceSequence, sequenceData: Map<String, *>, sequence: String) {
         if (!sequenceData.containsKey(segment.name)) {
             throw ProcessingValidationException("Missing the required segment '${segment.name}' in '$sequence'.")
         }
@@ -269,7 +267,7 @@ class ProcessedSequenceEntryValidator(
         }
     }
 
-    private fun <T> validateNoUnknownSegment(dataToValidate: Map<String, T>, sequenceGrouping: String) {
+    private fun validateNoUnknownSegment(dataToValidate: Map<String, *>, sequenceGrouping: String) {
         val unknownSegments = dataToValidate.keys.subtract(referenceGenome.nucleotideSequences.map { it.name }.toSet())
         if (unknownSegments.isNotEmpty()) {
             val unknownSegmentsString = unknownSegments.sorted().joinToString(", ")
@@ -279,7 +277,10 @@ class ProcessedSequenceEntryValidator(
         }
     }
 
-    private fun validateNoUnknownNucleotideSymbol(dataToValidate: Map<String, String?>, sequenceGrouping: String) {
+    private fun validateNoUnknownNucleotideSymbol(
+        dataToValidate: Map<String, NucleotideSequence?>,
+        sequenceGrouping: String,
+    ) {
         for ((segmentName, sequence) in dataToValidate) {
             if (sequence == null) {
                 continue
@@ -354,7 +355,7 @@ class ProcessedSequenceEntryValidator(
         }
     }
 
-    private fun validateNoUnknownAminoAcidSymbol(dataToValidate: Map<String, String?>) {
+    private fun validateNoUnknownAminoAcidSymbol(dataToValidate: Map<String, AminoAcidSequence?>) {
         for ((gene, sequence) in dataToValidate) {
             if (sequence == null) {
                 continue

diff --git a/backend/src/main/kotlin/org/loculus/backend/utils/FastaReader.kt b/backend/src/main/kotlin/org/loculus/backend/utils/FastaReader.kt
@@ -7,12 +7,11 @@ import java.io.InputStreamReader
 data class FastaEntry(val sampleName: String, val sequence: String)
 
 class FastaReader(inputStream: InputStream) : Iterator<FastaEntry>, Iterable<FastaEntry>, AutoCloseable {
-    private val reader: BufferedReader
+    private val reader: BufferedReader = BufferedReader(InputStreamReader(inputStream))
     private var nextEntry: FastaEntry? = null
     private var nextLine: String? = ""
 
     init {
-        reader = BufferedReader(InputStreamReader(inputStream))
         read()
     }