chore(deps): code style official renamed to intellij_idea; run ktlint…

…Format
loculus-project · Dec 6, 2023 · e680f46 · e680f46
1 parent 54a13ee
commit e680f46
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Showing 14 changed files with 236 additions and 330 deletions.
diff --git a/backend/.editorconfig b/backend/.editorconfig
@@ -6,7 +6,7 @@ insert_final_newline = true
 end_of_line = crlf
 
 [*.{kt,kts}]
-ktlint_code_style = official
+ktlint_code_style = intellij_idea
 trailing-comma-on-call-site = true
 trailing-comma-on-declaration-site = true
 ij_kotlin_allow_trailing_comma_on_call_site = true

diff --git a/backend/src/main/kotlin/org/pathoplexus/backend/config/Config.kt b/backend/src/main/kotlin/org/pathoplexus/backend/config/Config.kt
@@ -5,10 +5,9 @@ import org.pathoplexus.backend.api.Organism
 data class BackendConfig(
     val instances: Map<String, InstanceConfig>,
 ) {
-    fun getInstanceConfig(organism: Organism) =
-        instances[organism.name] ?: throw IllegalArgumentException(
-            "Organism: ${organism.name} not found in backend config. Available organisms: ${instances.keys}",
-        )
+    fun getInstanceConfig(organism: Organism) = instances[organism.name] ?: throw IllegalArgumentException(
+        "Organism: ${organism.name} not found in backend config. Available organisms: ${instances.keys}",
+    )
 }
 
 data class InstanceConfig(

diff --git a/backend/src/main/kotlin/org/pathoplexus/backend/model/SubmitModel.kt b/backend/src/main/kotlin/org/pathoplexus/backend/model/SubmitModel.kt
@@ -182,12 +182,7 @@ class SubmitModel(
         }
     }
 
-    private fun uploadSequences(
-        uploadId: String,
-        sequenceStream: InputStream,
-        batchSize: Int,
-        organism: Organism,
-    ) {
+    private fun uploadSequences(uploadId: String, sequenceStream: InputStream, batchSize: Int, organism: Organism) {
         log.info {
             "intermediate storing uploaded sequence data with UploadId $uploadId"
         }
@@ -238,10 +233,7 @@ class SubmitModel(
     }
 
     // TODO(#604): adapt revisions to the new flow
-    private fun processRevisedData(
-        metadataFile: MultipartFile,
-        sequenceFile: MultipartFile,
-    ): List<RevisedData> {
+    private fun processRevisedData(metadataFile: MultipartFile, sequenceFile: MultipartFile): List<RevisedData> {
         if (metadataFile.originalFilename == null || !metadataFile.originalFilename?.endsWith(".tsv")!!) {
             throw BadRequestException("Metadata file must have extension .tsv")
         }
@@ -263,10 +255,7 @@ class SubmitModel(
         }
     }
 
-    private fun validateHeaders(
-        metadataMap: Map<SubmissionId, Any>,
-        sequenceMap: Map<SubmissionId, Any>,
-    ) {
+    private fun validateHeaders(metadataMap: Map<SubmissionId, Any>, sequenceMap: Map<SubmissionId, Any>) {
         val metadataKeysSet = metadataMap.keys.toSet()
         val sequenceKeysSet = sequenceMap.keys.toSet()
         validateSubmissionIdSets(metadataKeysSet, sequenceKeysSet)

diff --git a/backend/src/main/kotlin/org/pathoplexus/backend/service/CompressionService.kt b/backend/src/main/kotlin/org/pathoplexus/backend/service/CompressionService.kt
@@ -25,11 +25,10 @@ class CompressionService(private val backendConfig: BackendConfig) {
         uncompressedSequence: String,
         segmentName: String,
         organism: Organism,
-    ): String =
-        compress(
-            uncompressedSequence,
-            getDictionaryForNucleotideSequenceSegments(segmentName, organism),
-        )
+    ): String = compress(
+        uncompressedSequence,
+        getDictionaryForNucleotideSequenceSegments(segmentName, organism),
+    )
 
     private fun decompressUnalignedNucleotideSequence(
         compressedSequence: String,
@@ -40,31 +39,29 @@ class CompressionService(private val backendConfig: BackendConfig) {
         getDictionaryForNucleotideSequenceSegments(segmentName, organism),
     )
 
-    fun decompressSequencesInOriginalData(originalData: OriginalData, organism: Organism) =
-        OriginalData(
-            originalData.metadata,
-            originalData
-                .unalignedNucleotideSequences.mapValues {
-                    decompressUnalignedNucleotideSequence(
-                        it.value,
-                        it.key,
-                        organism,
-                    )
-                },
-        )
+    fun decompressSequencesInOriginalData(originalData: OriginalData, organism: Organism) = OriginalData(
+        originalData.metadata,
+        originalData
+            .unalignedNucleotideSequences.mapValues {
+                decompressUnalignedNucleotideSequence(
+                    it.value,
+                    it.key,
+                    organism,
+                )
+            },
+    )
 
-    fun compressSequencesInOriginalData(originalData: OriginalData, organism: Organism) =
-        OriginalData(
-            originalData.metadata,
-            originalData
-                .unalignedNucleotideSequences.mapValues { (segmentName, sequenceData) ->
-                    compressUnalignedNucleotideSequence(
-                        sequenceData,
-                        segmentName,
-                        organism,
-                    )
-                },
-        )
+    fun compressSequencesInOriginalData(originalData: OriginalData, organism: Organism) = OriginalData(
+        originalData.metadata,
+        originalData
+            .unalignedNucleotideSequences.mapValues { (segmentName, sequenceData) ->
+                compressUnalignedNucleotideSequence(
+                    sequenceData,
+                    segmentName,
+                    organism,
+                )
+            },
+    )
 
     private fun compress(seq: String, dictionary: ByteArray?): String {
         val input = seq.toByteArray(StandardCharsets.UTF_8)
@@ -99,13 +96,11 @@ class CompressionService(private val backendConfig: BackendConfig) {
         return String(decompressedBuffer, 0, decompressionReturnCode.toInt(), StandardCharsets.UTF_8)
     }
 
-    private fun getDictionaryForNucleotideSequenceSegments(
-        segmentName: String,
-        organism: Organism,
-    ): ByteArray? = backendConfig
-        .getInstanceConfig(organism)
-        .referenceGenomes
-        .getNucleotideSegmentReference(
-            segmentName,
-        )?.toByteArray()
+    private fun getDictionaryForNucleotideSequenceSegments(segmentName: String, organism: Organism): ByteArray? =
+        backendConfig
+            .getInstanceConfig(organism)
+            .referenceGenomes
+            .getNucleotideSegmentReference(
+                segmentName,
+            )?.toByteArray()
 }
diff --git a/backend/src/main/kotlin/org/pathoplexus/backend/service/DatabaseService.kt b/backend/src/main/kotlin/org/pathoplexus/backend/service/DatabaseService.kt
@@ -189,9 +189,7 @@ class DatabaseService(
         }
     }
 
-    private fun addMissingKeysForInsertions(
-        submittedProcessedData: SubmittedProcessedData,
-    ): SubmittedProcessedData {
+    private fun addMissingKeysForInsertions(submittedProcessedData: SubmittedProcessedData): SubmittedProcessedData {
         val nucleotideInsertions = referenceGenome.nucleotideSequences.associate {
             if (it.name in submittedProcessedData.data.nucleotideInsertions.keys) {
                 it.name to submittedProcessedData.data.nucleotideInsertions[it.name]!!

diff --git a/backend/src/main/kotlin/org/pathoplexus/backend/service/SequenceValidator.kt b/backend/src/main/kotlin/org/pathoplexus/backend/service/SequenceValidator.kt
@@ -89,9 +89,7 @@ class SequenceValidator(
         validateAminoAcidSequences(submittedProcessedData)
     }
 
-    private fun validateMetadata(
-        submittedProcessedData: SubmittedProcessedData,
-    ) {
+    private fun validateMetadata(submittedProcessedData: SubmittedProcessedData) {
         val metadataFields = schema.metadata
         validateNoUnknownInMetaData(submittedProcessedData.data.metadata, metadataFields.map { it.name })
 
@@ -100,21 +98,15 @@ class SequenceValidator(
         }
     }
 
-    private fun <T> validateNoUnknownInMetaData(
-        data: Map<String, T>,
-        known: List<String>,
-    ) {
+    private fun <T> validateNoUnknownInMetaData(data: Map<String, T>, known: List<String>) {
         val unknownMetadataKeys = data.keys.subtract(known.toSet())
         if (unknownMetadataKeys.isNotEmpty()) {
             val unknownMetadataKeysString = unknownMetadataKeys.sorted().joinToString(", ")
             throw ProcessingValidationException("Unknown fields in processed data: $unknownMetadataKeysString.")
         }
     }
 
-    private fun validateKnownMetadataField(
-        metadata: Metadata,
-        submittedProcessedData: SubmittedProcessedData,
-    ) {
+    private fun validateKnownMetadataField(metadata: Metadata, submittedProcessedData: SubmittedProcessedData) {
         val fieldName = metadata.name
         val fieldValue = submittedProcessedData.data.metadata[fieldName]
 
@@ -192,9 +184,7 @@ class SequenceValidator(
         return pangoLineageCandidate.matches(pangoLineageRegex)
     }
 
-    private fun validateNucleotideSequences(
-        submittedProcessedData: SubmittedProcessedData,
-    ) {
+    private fun validateNucleotideSequences(submittedProcessedData: SubmittedProcessedData) {
         for (segment in referenceGenome.nucleotideSequences) {
             validateNoMissingSegment(
                 segment,
@@ -268,10 +258,7 @@ class SequenceValidator(
         }
     }
 
-    private fun <T> validateNoUnknownSegment(
-        dataToValidate: Map<String, T>,
-        sequenceGrouping: String,
-    ) {
+    private fun <T> validateNoUnknownSegment(dataToValidate: Map<String, T>, sequenceGrouping: String) {
         val unknownSegments = dataToValidate.keys.subtract(referenceGenome.nucleotideSequences.map { it.name }.toSet())
         if (unknownSegments.isNotEmpty()) {
             val unknownSegmentsString = unknownSegments.sorted().joinToString(", ")
@@ -281,10 +268,7 @@ class SequenceValidator(
         }
     }
 
-    private fun validateNoUnknownNucleotideSymbol(
-        dataToValidate: Map<String, String>,
-        sequenceGrouping: String,
-    ) {
+    private fun validateNoUnknownNucleotideSymbol(dataToValidate: Map<String, String>, sequenceGrouping: String) {
         for (sequence in dataToValidate) {
             val invalidSymbols = sequence.value.getInvalidSymbols<NucleotideSymbols>()
             if (invalidSymbols.isNotEmpty()) {
@@ -296,9 +280,7 @@ class SequenceValidator(
         }
     }
 
-    private fun validateNoUnknownNucleotideSymbolInInsertion(
-        dataToValidate: Map<String, List<Insertion>>,
-    ) {
+    private fun validateNoUnknownNucleotideSymbolInInsertion(dataToValidate: Map<String, List<Insertion>>) {
         for (sequence in dataToValidate) {
             for (insertion in sequence.value) {
                 val invalidSymbols = insertion.sequence.getInvalidSymbols<NucleotideSymbols>()
@@ -320,9 +302,7 @@ class SequenceValidator(
         where ValidSymbols : Enum<ValidSymbols>, ValidSymbols : Symbol =
         enumValues<ValidSymbols>().any { it.symbol == this }
 
-    private fun validateAminoAcidSequences(
-        submittedProcessedData: SubmittedProcessedData,
-    ) {
+    private fun validateAminoAcidSequences(submittedProcessedData: SubmittedProcessedData) {
         for (gene in referenceGenome.genes) {
             validateNoMissingGene(gene, submittedProcessedData)
             validateLengthOfSequence(
@@ -346,29 +326,21 @@ class SequenceValidator(
         validateNoUnknownAminoAcidSymbolInInsertion(submittedProcessedData.data.aminoAcidInsertions)
     }
 
-    private fun validateNoMissingGene(
-        gene: ReferenceSequence,
-        submittedProcessedData: SubmittedProcessedData,
-    ) {
+    private fun validateNoMissingGene(gene: ReferenceSequence, submittedProcessedData: SubmittedProcessedData) {
         if (!submittedProcessedData.data.alignedAminoAcidSequences.containsKey(gene.name)) {
             throw ProcessingValidationException("Missing the required gene '${gene.name}'.")
         }
     }
 
-    private fun validateNoUnknownGeneInData(
-        data: Map<String, *>,
-        geneGrouping: String,
-    ) {
+    private fun validateNoUnknownGeneInData(data: Map<String, *>, geneGrouping: String) {
         val unknownGenes = data.keys.subtract(referenceGenome.genes.map { it.name }.toSet())
         if (unknownGenes.isNotEmpty()) {
             val unknownGenesString = unknownGenes.sorted().joinToString(", ")
             throw ProcessingValidationException("Unknown genes in '$geneGrouping': $unknownGenesString.")
         }
     }
 
-    private fun validateNoUnknownAminoAcidSymbol(
-        dataToValidate: Map<String, String>,
-    ) {
+    private fun validateNoUnknownAminoAcidSymbol(dataToValidate: Map<String, String>) {
         for (sequence in dataToValidate) {
             val invalidSymbols = sequence.value.getInvalidSymbols<AminoAcidSymbols>()
             if (invalidSymbols.isNotEmpty()) {
@@ -380,9 +352,7 @@ class SequenceValidator(
         }
     }
 
-    private fun validateNoUnknownAminoAcidSymbolInInsertion(
-        dataToValidate: Map<String, List<Insertion>>,
-    ) {
+    private fun validateNoUnknownAminoAcidSymbolInInsertion(dataToValidate: Map<String, List<Insertion>>) {
         for (sequence in dataToValidate) {
             for (insertion in sequence.value) {
                 val invalidSymbols = insertion.sequence.getInvalidSymbols<AminoAcidSymbols>()

diff --git a/backend/src/main/kotlin/org/pathoplexus/backend/utils/IteratorStreamer.kt b/backend/src/main/kotlin/org/pathoplexus/backend/utils/IteratorStreamer.kt
@@ -12,10 +12,7 @@ class IteratorStreamer(private val objectMapper: ObjectMapper) {
     fun <T> streamAsNdjson(iterable: Iterable<T>, outputStream: OutputStream) =
         streamAsNdjson(iterable.iterator(), outputStream)
 
-    fun <T> streamAsNdjson(
-        iterator: Iterator<T>,
-        outputStream: OutputStream,
-    ) {
+    fun <T> streamAsNdjson(iterator: Iterator<T>, outputStream: OutputStream) {
         iterator.forEach {
             val json = objectMapper.writeValueAsString(it)
             outputStream.write(json.toByteArray())

diff --git a/backend/src/test/kotlin/org/pathoplexus/backend/controller/GetReleasedDataEndpointTest.kt b/backend/src/test/kotlin/org/pathoplexus/backend/controller/GetReleasedDataEndpointTest.kt
@@ -22,7 +22,7 @@ import org.springframework.test.web.servlet.result.MockMvcResultMatchers.status
 import java.time.LocalDateTime
 import java.time.format.DateTimeFormatter
 
-private const val numberOfFieldsWithUnknownValue = 2
+private const val NUMBER_OF_FIELDS_WITH_UNKNOWN_VALUE = 2
 
 @EndpointTest
 class GetReleasedDataEndpointTest(
@@ -77,7 +77,7 @@ class GetReleasedDataEndpointTest(
                 "versionStatus" to TextNode("LATEST_VERSION"),
             )
 
-            assertThat(it.metadata.size, `is`(expectedMetadata.size + numberOfFieldsWithUnknownValue))
+            assertThat(it.metadata.size, `is`(expectedMetadata.size + NUMBER_OF_FIELDS_WITH_UNKNOWN_VALUE))
             for ((key, value) in it.metadata) {
                 when (key) {
                     "submittedAt" -> {