feat: transform lower case sequences to upper case

loculus-project · Aug 26, 2024 · 1951075 · 1951075
1 parent 9860996
commit 1951075
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Showing 3 changed files with 72 additions and 3 deletions.
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
@@ -75,6 +75,7 @@ import org.springframework.transaction.annotation.Transactional
 import java.io.BufferedReader
 import java.io.InputStream
 import java.io.InputStreamReader
+import java.util.Locale
 import javax.sql.DataSource
 
 private val log = KotlinLogging.logger { }
@@ -318,7 +319,7 @@ class SubmissionDatabaseService(
         val submittedWarnings = submittedProcessedData.warnings.orEmpty()
 
         val (newStatus, processedData) = when {
-            submittedErrors.isEmpty() -> FINISHED to validateProcessedData(
+            submittedErrors.isEmpty() -> FINISHED to postprocessAndValidateProcessedData(
                 submittedProcessedData,
                 organism,
             )
@@ -349,13 +350,35 @@ class SubmissionDatabaseService(
         return newStatus
     }
 
-    private fun validateProcessedData(submittedProcessedData: SubmittedProcessedData, organism: Organism) = try {
+    private fun postprocessAndValidateProcessedData(
+        submittedProcessedData: SubmittedProcessedData,
+        organism: Organism,
+    ) = try {
         throwIfIsSubmissionForWrongOrganism(submittedProcessedData, organism)
-        processedSequenceEntryValidatorFactory.create(organism).validate(submittedProcessedData.data)
+        val processedData = makeSequencesUpperCase(submittedProcessedData.data)
+        processedSequenceEntryValidatorFactory.create(organism).validate(processedData)
     } catch (validationException: ProcessingValidationException) {
         throw validationException
     }
 
+    private fun makeSequencesUpperCase(processedData: ProcessedData<GeneticSequence>) = processedData.copy(
+        unalignedNucleotideSequences = processedData.unalignedNucleotideSequences.mapValues { (_, it) ->
+            it?.uppercase(Locale.US)
+        },
+        alignedNucleotideSequences = processedData.alignedNucleotideSequences.mapValues { (_, it) ->
+            it?.uppercase(Locale.US)
+        },
+        alignedAminoAcidSequences = processedData.alignedAminoAcidSequences.mapValues { (_, it) ->
+            it?.uppercase(Locale.US)
+        },
+        nucleotideInsertions = processedData.nucleotideInsertions.mapValues { (_, it) ->
+            it.map { insertion -> insertion.copy(sequence = insertion.sequence.uppercase(Locale.US)) }
+        },
+        aminoAcidInsertions = processedData.aminoAcidInsertions.mapValues { (_, it) ->
+            it.map { insertion -> insertion.copy(sequence = insertion.sequence.uppercase(Locale.US)) }
+        },
+    )
+
     private fun validateExternalMetadata(
         externalSubmittedData: ExternalSubmittedData,
         organism: Organism,

diff --git a/backend/src/test/kotlin/org/loculus/backend/controller/submission/PreparedProcessedData.kt b/backend/src/test/kotlin/org/loculus/backend/controller/submission/PreparedProcessedData.kt
@@ -141,6 +141,30 @@ object PreparedProcessedData {
         ),
     )
 
+    fun withLowercaseSequences(accession: Accession, version: Version) = defaultSuccessfulSubmittedData.copy(
+        accession = accession,
+        version = version,
+        data = defaultProcessedData.copy(
+            unalignedNucleotideSequences = mapOf(
+                MAIN_SEGMENT to "nactg",
+            ),
+            alignedNucleotideSequences = mapOf(
+                MAIN_SEGMENT to "attaaaggtttataccttcccaggtaacaaaccaaccaactttcgatct",
+            ),
+            nucleotideInsertions = mapOf(
+                MAIN_SEGMENT to listOf(Insertion(123, "actg")),
+            ),
+            alignedAminoAcidSequences = mapOf(
+                SOME_LONG_GENE to "acdefghiklmnpqrstvwybzx-*",
+                SOME_SHORT_GENE to "mads",
+            ),
+            aminoAcidInsertions = mapOf(
+                SOME_LONG_GENE to listOf(Insertion(123, "def")),
+                SOME_SHORT_GENE to listOf(Insertion(123, "n")),
+            ),
+        ),
+    )
+
     fun withMissingMetadataFields(
         accession: Accession,
         version: Long = defaultSuccessfulSubmittedData.version,

diff --git a/.../test/kotlin/org/loculus/backend/controller/submission/SubmitProcessedDataEndpointTest.kt b/.../test/kotlin/org/loculus/backend/controller/submission/SubmitProcessedDataEndpointTest.kt
@@ -90,6 +90,28 @@ class SubmitProcessedDataEndpointTest(
             .assertStatusIs(Status.AWAITING_APPROVAL)
     }
 
+    @Test
+    fun `WHEN I submit data with lowercase sequences THEN the sequences are converted to uppercase`() {
+        val (accession, version) = prepareExtractedSequencesInDatabase().first()
+
+        submissionControllerClient.submitProcessedData(
+            PreparedProcessedData.withLowercaseSequences(accession = accession, version = version),
+        )
+            .andExpect(status().isNoContent)
+
+        val processedData = convenienceClient.getSequenceEntryToEdit(accession = accession, version = version)
+            .processedData
+
+        assertThat(processedData.unalignedNucleotideSequences, hasEntry(MAIN_SEGMENT, "NACTG"))
+        assertThat(
+            processedData.alignedNucleotideSequences,
+            hasEntry(MAIN_SEGMENT, "ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCT"),
+        )
+        assertThat(processedData.alignedAminoAcidSequences, hasEntry(SOME_LONG_GENE, "ACDEFGHIKLMNPQRSTVWYBZX-*"))
+        assertThat(processedData.nucleotideInsertions, hasEntry(MAIN_SEGMENT, listOf(Insertion(123, "ACTG"))))
+        assertThat(processedData.aminoAcidInsertions, hasEntry(SOME_LONG_GENE, listOf(Insertion(123, "DEF"))))
+    }
+
     @Test
     fun `WHEN I submit with all valid symbols THEN the sequence entry is in status processed`() {
         val accessions = prepareExtractedSequencesInDatabase().map { it.accession }