feat: add alignedNucleotideSequence, aminoAcidSequence endpoints

Author: Jonas Kellerer

.idea/runConfigurations/LapisV2Open.xml

@@ -79,8 +79,9 @@ openApi {
     apiDocsUrl.set("http://localhost:8080/api-docs")
     customBootRun {
         args.set([
-            "--silo.url=does.not.matter.here",
-            "--lapis.databaseConfig.path=../siloLapisTests/testData/testDatabaseConfig.yaml"
+                "--silo.url=does.not.matter.here",
+                "--lapis.databaseConfig.path=../siloLapisTests/testData/testDatabaseConfig.yaml",
+                "--referenceGenomeFilename=../siloLapisTests/testData/reference-genomes.json"
         ])
     }
 }

.idea/runConfigurations/LapisV2Protected.xml

@@ -4,12 +4,16 @@ services:
     image: ghcr.io/genspectrum/lapis-v2:${LAPIS_TAG}
     ports:
       - "8080:8080"
-    command: --silo.url=http://silo:8081 --lapis.databaseConfig.path=databaseConfig.yaml
+    command: --silo.url=http://silo:8081 --lapis.databaseConfig.path=databaseConfig.yaml --referenceGenomeFilename=reference-genomes.json
     volumes:
       - type: bind
         source: ../siloLapisTests/testData/testDatabaseConfig.yaml
         target: /workspace/databaseConfig.yaml
         read_only: true
+      - type: bind
+        source: ../siloLapisTests/testData/reference-genomes.json
+        target: /workspace/reference-genomes.json
+        read_only: true
 
   silo:
     image: ghcr.io/genspectrum/lapis-silo:${SILO_TAG}

lapis2/build.gradle

@@ -1,11 +1,14 @@
 package org.genspectrum.lapis
 
+import org.genspectrum.lapis.config.ReferenceGenome
 import org.springframework.boot.autoconfigure.SpringBootApplication
 import org.springframework.boot.runApplication
 
 @SpringBootApplication
 class Lapisv2Application
 
 fun main(args: Array<String>) {
-    runApplication<Lapisv2Application>(*args)
+    val referenceGenomeArgs = ReferenceGenome.readFromFileFromProgramArgs(args).toSpringApplicationArgs()
+
+    runApplication<Lapisv2Application>(*(args + referenceGenomeArgs))
 }

lapis2/docker-compose.yml

@@ -4,6 +4,9 @@ import com.fasterxml.jackson.module.kotlin.readValue
 import mu.KotlinLogging
 import org.genspectrum.lapis.auth.DataOpennessAuthorizationFilterFactory
 import org.genspectrum.lapis.config.DatabaseConfig
+import org.genspectrum.lapis.config.NucleotideSequence
+import org.genspectrum.lapis.config.REFERENCE_GENOME_APPLICATION_ARG_PREFIX
+import org.genspectrum.lapis.config.ReferenceGenome
 import org.genspectrum.lapis.config.SequenceFilterFields
 import org.genspectrum.lapis.logging.RequestContext
 import org.genspectrum.lapis.logging.RequestContextLogger
@@ -60,4 +63,11 @@ class LapisSpringConfig {
     fun dataOpennessAuthorizationFilter(
         dataOpennessAuthorizationFilterFactory: DataOpennessAuthorizationFilterFactory,
     ) = dataOpennessAuthorizationFilterFactory.create()
+
+    @Bean
+    fun referenceGenome(
+        @Value("\${$REFERENCE_GENOME_APPLICATION_ARG_PREFIX}") nucleotideSegments: List<String>,
+    ): ReferenceGenome {
+        return ReferenceGenome(nucleotideSegments.map { NucleotideSequence(it) })
+    }
 }

lapis2/src/main/kotlin/org/genspectrum/lapis/LapisApplication.kt

@@ -42,6 +42,7 @@ import org.genspectrum.lapis.controller.ORDER_BY_FIELDS_SCHEMA
 import org.genspectrum.lapis.controller.ORDER_BY_PROPERTY
 import org.genspectrum.lapis.controller.REQUEST_SCHEMA_WITH_MIN_PROPORTION
 import org.genspectrum.lapis.controller.SEQUENCE_FILTERS_SCHEMA
+import org.genspectrum.lapis.controller.SEQUENCE_REQUEST_SCHEMA
 import org.genspectrum.lapis.request.AminoAcidInsertion
 import org.genspectrum.lapis.request.AminoAcidMutation
 import org.genspectrum.lapis.request.NucleotideInsertion
@@ -64,8 +65,9 @@ fun buildOpenApiSchema(sequenceFilterFields: SequenceFilterFields, databaseConfi
         Pair(AMINO_ACID_INSERTIONS_PROPERTY, aminoAcidInsertions()) +
         Pair(ORDER_BY_PROPERTY, orderByPostSchema()) +
         Pair(LIMIT_PROPERTY, limitSchema()) +
-        Pair(OFFSET_PROPERTY, offsetSchema()) +
-        Pair(FORMAT_PROPERTY, formatSchema())
+        Pair(OFFSET_PROPERTY, offsetSchema())
+
+    val sequenceFiltersWithFormat = sequenceFilters + Pair(FORMAT_PROPERTY, formatSchema())
 
     return OpenAPI()
         .components(
@@ -82,18 +84,24 @@ fun buildOpenApiSchema(sequenceFilterFields: SequenceFilterFields, databaseConfi
                     Schema<String>()
                         .type("object")
                         .description("valid filters for sequence data")
-                        .properties(sequenceFilters + Pair(MIN_PROPORTION_PROPERTY, Schema<String>().type("number"))),
+                        .properties(
+                            sequenceFiltersWithFormat + Pair(MIN_PROPORTION_PROPERTY, Schema<String>().type("number")),
+                        ),
                 )
                 .addSchemas(
                     AGGREGATED_REQUEST_SCHEMA,
-                    requestSchemaWithFields(sequenceFilters, AGGREGATED_GROUP_BY_FIELDS_DESCRIPTION),
+                    requestSchemaWithFields(sequenceFiltersWithFormat, AGGREGATED_GROUP_BY_FIELDS_DESCRIPTION),
                 )
                 .addSchemas(
                     DETAILS_REQUEST_SCHEMA,
-                    requestSchemaWithFields(sequenceFilters, DETAILS_FIELDS_DESCRIPTION),
+                    requestSchemaWithFields(sequenceFiltersWithFormat, DETAILS_FIELDS_DESCRIPTION),
                 )
                 .addSchemas(
                     INSERTIONS_REQUEST_SCHEMA,
+                    requestSchemaForCommonSequenceFilters(sequenceFiltersWithFormat),
+                )
+                .addSchemas(
+                    SEQUENCE_REQUEST_SCHEMA,
                     requestSchemaForCommonSequenceFilters(sequenceFilters),
                 )
                 .addSchemas(

lapis2/src/main/kotlin/org/genspectrum/lapis/LapisSpringConfig.kt

@@ -9,8 +9,13 @@ import org.genspectrum.lapis.config.AccessKeysReader
 import org.genspectrum.lapis.config.DatabaseConfig
 import org.genspectrum.lapis.config.OpennessLevel
 import org.genspectrum.lapis.controller.ACCESS_KEY_PROPERTY
+import org.genspectrum.lapis.controller.AGGREGATED_ROUTE
+import org.genspectrum.lapis.controller.AMINO_ACID_INSERTIONS_ROUTE
+import org.genspectrum.lapis.controller.AMINO_ACID_MUTATIONS_ROUTE
 import org.genspectrum.lapis.controller.LapisError
 import org.genspectrum.lapis.controller.LapisErrorResponse
+import org.genspectrum.lapis.controller.NUCLEOTIDE_INSERTIONS_ROUTE
+import org.genspectrum.lapis.controller.NUCLEOTIDE_MUTATIONS_ROUTE
 import org.genspectrum.lapis.util.CachedBodyHttpServletRequest
 import org.springframework.http.HttpStatus
 import org.springframework.http.MediaType
@@ -93,7 +98,13 @@ private class ProtectedDataAuthorizationFilter(
 
     companion object {
         private val WHITELISTED_PATHS = listOf("/swagger-ui", "/api-docs")
-        private val ENDPOINTS_THAT_SERVE_AGGREGATED_DATA = listOf("/aggregated", "/nucleotideMutations")
+        private val ENDPOINTS_THAT_SERVE_AGGREGATED_DATA = listOf(
+            AGGREGATED_ROUTE,
+            NUCLEOTIDE_MUTATIONS_ROUTE,
+            AMINO_ACID_MUTATIONS_ROUTE,
+            NUCLEOTIDE_INSERTIONS_ROUTE,
+            AMINO_ACID_INSERTIONS_ROUTE,
+        )
     }
 
     override fun isAuthorizedForEndpoint(request: CachedBodyHttpServletRequest): AuthorizationResult {

lapis2/src/main/kotlin/org/genspectrum/lapis/OpenApiDocs.kt

@@ -0,0 +1,53 @@
+package org.genspectrum.lapis.config
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties
+import com.fasterxml.jackson.annotation.JsonProperty
+import com.fasterxml.jackson.module.kotlin.jacksonObjectMapper
+import com.fasterxml.jackson.module.kotlin.readValue
+import java.io.File
+
+const val REFERENCE_GENOME_APPLICATION_ARG_PREFIX = "referenceGenome.nucleotideSequences"
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+class ReferenceGenome(
+    @JsonProperty("nucleotide_sequences")
+    val nucleotideSequences: List<NucleotideSequence>,
+) {
+    fun isSingleSegmented(): Boolean {
+        return nucleotideSequences.size == 1
+    }
+
+    companion object {
+        fun readFromFile(filename: String): ReferenceGenome {
+            return jacksonObjectMapper().readValue(File(filename))
+        }
+
+        private fun readFilenameFromProgramArgs(args: Array<String>): String {
+            val referenceGenomeArg = args.find { it.startsWith("--referenceGenomeFilename=") }
+            return referenceGenomeArg?.substringAfter("=") ?: throw IllegalArgumentException(
+                "No reference genome filename specified. Please specify a reference genome filename using the " +
+                    "--referenceGenomeFilename argument.",
+            )
+        }
+
+        fun readFromFileFromProgramArgs(args: Array<String>): ReferenceGenome {
+            return readFromFile(readFilenameFromProgramArgs(args))
+        }
+    }
+
+    fun toSpringApplicationArgs(): Array<String> {
+        val nucleotideSequenceArgs =
+            "--$REFERENCE_GENOME_APPLICATION_ARG_PREFIX=" + this.nucleotideSequences.joinToString(
+                separator = ",",
+            ) {
+                it.name
+            }
+
+        return arrayOf(nucleotideSequenceArgs)
+    }
+}
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+data class NucleotideSequence(
+    val name: String,
+)