feat: provide full reference genome, and database config to new endpo…

…ints

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

@@ -1,17 +1,19 @@
 package org.genspectrum.lapis
 
-import org.genspectrum.lapis.config.ReferenceGenome
+import org.genspectrum.lapis.config.ReferenceGenomeSchema
 import org.springframework.boot.autoconfigure.SpringBootApplication
 import org.springframework.boot.runApplication
 
 @SpringBootApplication
 class Lapisv2Application
 
 fun main(args: Array<String>) {
-    val referenceGenomeArgs = ReferenceGenome.readFromFileFromProgramArgsOrEnv(args).toSpringApplicationArgs()
+    val referenceGenomeSchemaArgs = ReferenceGenomeSchema.readFromFileFromProgramArgsOrEnv(
+        args,
+    ).toSpringApplicationArgs()
 
     try {
-        runApplication<Lapisv2Application>(*(args + referenceGenomeArgs))
+        runApplication<Lapisv2Application>(*(args + referenceGenomeSchemaArgs))
     } catch (e: Exception) {
         e.printStackTrace()
         throw e

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

@@ -4,10 +4,14 @@ 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.NO_REFERENCE_GENOME_FILENAME_ERROR_MESSAGE
+import org.genspectrum.lapis.config.REFERENCE_GENOME_ENV_VARIABLE_NAME
+import org.genspectrum.lapis.config.REFERENCE_GENOME_FILENAME_ARGS_NAME
 import org.genspectrum.lapis.config.REFERENCE_GENOME_GENES_APPLICATION_ARG_PREFIX
 import org.genspectrum.lapis.config.REFERENCE_GENOME_SEGMENTS_APPLICATION_ARG_PREFIX
 import org.genspectrum.lapis.config.ReferenceGenome
-import org.genspectrum.lapis.config.ReferenceSequence
+import org.genspectrum.lapis.config.ReferenceGenomeSchema
+import org.genspectrum.lapis.config.ReferenceSequenceSchema
 import org.genspectrum.lapis.config.SequenceFilterFields
 import org.genspectrum.lapis.logging.RequestContext
 import org.genspectrum.lapis.logging.RequestContextLogger
@@ -27,8 +31,8 @@ class LapisSpringConfig {
     fun openAPI(
         sequenceFilterFields: SequenceFilterFields,
         databaseConfig: DatabaseConfig,
-        referenceGenome: ReferenceGenome,
-    ) = buildOpenApiSchema(sequenceFilterFields, databaseConfig, referenceGenome)
+        referenceGenomeSchema: ReferenceGenomeSchema,
+    ) = buildOpenApiSchema(sequenceFilterFields, databaseConfig, referenceGenomeSchema)
 
     @Bean
     fun databaseConfig(
@@ -70,11 +74,22 @@ class LapisSpringConfig {
     ) = dataOpennessAuthorizationFilterFactory.create()
 
     @Bean
-    fun referenceGenome(
+    fun referenceGenomeSchema(
         @Value("\${$REFERENCE_GENOME_SEGMENTS_APPLICATION_ARG_PREFIX}") nucleotideSegments: List<String>,
         @Value("\${$REFERENCE_GENOME_GENES_APPLICATION_ARG_PREFIX}") genes: List<String>,
-    ) = ReferenceGenome(
-        nucleotideSegments.map { ReferenceSequence(it) },
-        genes.map { ReferenceSequence(it) },
+    ) = ReferenceGenomeSchema(
+        nucleotideSegments.map { ReferenceSequenceSchema(it) },
+        genes.map { ReferenceSequenceSchema(it) },
     )
+
+    @Bean
+    fun referenceGenome(
+        @Value("\${$REFERENCE_GENOME_FILENAME_ARGS_NAME:#{null}}") referenceGenomeFilename: String?,
+    ): ReferenceGenome {
+        val filename = referenceGenomeFilename
+            ?: System.getenv(REFERENCE_GENOME_ENV_VARIABLE_NAME)
+            ?: throw IllegalArgumentException(NO_REFERENCE_GENOME_FILENAME_ERROR_MESSAGE)
+
+        return ReferenceGenome.readFromFile(filename)
+    }
 }

lapis2/src/main/kotlin/org/genspectrum/lapis/config/ReferenceGenome.kt

@@ -9,22 +9,30 @@ import java.io.File
 const val REFERENCE_GENOME_SEGMENTS_APPLICATION_ARG_PREFIX = "referenceGenome.segments"
 const val REFERENCE_GENOME_GENES_APPLICATION_ARG_PREFIX = "referenceGenome.genes"
 
-private const val ENV_VARIABLE_NAME = "LAPIS_REFERENCE_GENOME_FILENAME"
-private const val ARGS_NAME = "referenceGenomeFilename"
+const val REFERENCE_GENOME_ENV_VARIABLE_NAME = "LAPIS_REFERENCE_GENOME_FILENAME"
+const val REFERENCE_GENOME_FILENAME_ARGS_NAME = "referenceGenomeFilename"
+
+const val NO_REFERENCE_GENOME_FILENAME_ERROR_MESSAGE =
+    """No reference genome filename specified.
+    Please specify a reference genome filename using the --$REFERENCE_GENOME_FILENAME_ARGS_NAME argument 
+    or the $REFERENCE_GENOME_ENV_VARIABLE_NAME environment variable."""
 
 @JsonIgnoreProperties(ignoreUnknown = true)
-class ReferenceGenome(val nucleotideSequences: List<ReferenceSequence>, val genes: List<ReferenceSequence>) {
-    private val nucleotideSequenceNames: Map<LowercaseName, ReferenceSequence> = nucleotideSequences
+class ReferenceGenomeSchema(
+    val nucleotideSequences: List<ReferenceSequenceSchema>,
+    val genes: List<ReferenceSequenceSchema>,
+) {
+    private val nucleotideSequenceNames: Map<LowercaseName, ReferenceSequenceSchema> = nucleotideSequences
         .associateBy { it.name.lowercase() }
-    private val geneNames: Map<LowercaseName, ReferenceSequence> = genes
+    private val geneNames: Map<LowercaseName, ReferenceSequenceSchema> = genes
         .associateBy { it.name.lowercase() }
 
-    fun getNucleotideSequenceFromLowercaseName(lowercaseName: LowercaseName): ReferenceSequence {
+    fun getNucleotideSequenceFromLowercaseName(lowercaseName: LowercaseName): ReferenceSequenceSchema {
         return nucleotideSequenceNames[lowercaseName]
             ?: throw BadRequestException("Unknown nucleotide sequence from lower case: $lowercaseName")
     }
 
-    fun getGeneFromLowercaseName(lowercaseName: LowercaseName): ReferenceSequence {
+    fun getGeneFromLowercaseName(lowercaseName: LowercaseName): ReferenceSequenceSchema {
         return geneNames[lowercaseName]
             ?: throw BadRequestException("Unknown gene from lower case: $lowercaseName")
     }
@@ -34,23 +42,20 @@ class ReferenceGenome(val nucleotideSequences: List<ReferenceSequence>, val gene
     }
 
     companion object {
-        fun readFromFileFromProgramArgsOrEnv(args: Array<String>): ReferenceGenome {
+        fun readFromFileFromProgramArgsOrEnv(args: Array<String>): ReferenceGenomeSchema {
             val filename = readFilenameFromProgramArgs(args)
-                ?: System.getenv(ENV_VARIABLE_NAME)
-                ?: throw IllegalArgumentException(
-                    "No reference genome filename specified. Please specify a reference genome filename using the " +
-                        "--$ARGS_NAME argument or the $ENV_VARIABLE_NAME environment variable.",
-                )
+                ?: System.getenv(REFERENCE_GENOME_ENV_VARIABLE_NAME)
+                ?: throw IllegalArgumentException(NO_REFERENCE_GENOME_FILENAME_ERROR_MESSAGE)
 
             return readFromFile(filename)
         }
 
-        fun readFromFile(filename: String): ReferenceGenome {
+        fun readFromFile(filename: String): ReferenceGenomeSchema {
             return jacksonObjectMapper().readValue(File(filename))
         }
 
         private fun readFilenameFromProgramArgs(args: Array<String>): String? {
-            val referenceGenomeArg = args.find { it.startsWith("--$ARGS_NAME=") }
+            val referenceGenomeArg = args.find { it.startsWith("--$REFERENCE_GENOME_FILENAME_ARGS_NAME=") }
             return referenceGenomeArg?.substringAfter("=")
         }
     }
@@ -66,6 +71,22 @@ class ReferenceGenome(val nucleotideSequences: List<ReferenceSequence>, val gene
 }
 
 @JsonIgnoreProperties(ignoreUnknown = true)
+data class ReferenceSequenceSchema(
+    val name: String,
+)
+
+data class ReferenceGenome(
+    val nucleotideSequences: List<ReferenceSequence>,
+    val genes: List<ReferenceSequence>,
+) {
+    companion object {
+        fun readFromFile(filename: String): ReferenceGenome {
+            return jacksonObjectMapper().readValue(File(filename))
+        }
+    }
+}
+
 data class ReferenceSequence(
     val name: String,
+    val sequence: String,
 )

lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ControllerDescriptions.kt

@@ -17,7 +17,9 @@ const val AMINO_ACID_INSERTIONS_ENDPOINT_DESCRIPTION =
     """Returns a list of mutations along with the counts and proportions whose proportions are greater 
     than or equal to the specified minProportion. Only sequences matching the specified sequence filters are
     considered."""
-const val INFO_ENDPOINT_DESCRIPTION = "Returns information about LAPIS"
+const val INFO_ENDPOINT_DESCRIPTION = "Returns information about LAPIS."
+const val DATABASE_CONFIG_ENDPOINT_DESCRIPTION = "Returns the database configuration."
+const val REFERENCE_GENOME_ENDPOINT_DESCRIPTION = "Returns the reference genome."
 const val ALIGNED_AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION =
     """Returns a string of fasta formated aligned amino acid sequences. Only sequences matching the specified
     sequence filters are considered."""

lapis2/src/main/kotlin/org/genspectrum/lapis/controller/InfoController.kt

@@ -1,6 +1,8 @@
 package org.genspectrum.lapis.controller
 
 import io.swagger.v3.oas.annotations.Operation
+import org.genspectrum.lapis.config.DatabaseConfig
+import org.genspectrum.lapis.config.ReferenceGenome
 import org.genspectrum.lapis.model.SiloQueryModel
 import org.genspectrum.lapis.request.LapisInfo
 import org.springframework.http.MediaType
@@ -9,14 +11,28 @@ import org.springframework.web.bind.annotation.RequestMapping
 import org.springframework.web.bind.annotation.RestController
 
 const val INFO_ROUTE = "/info"
+const val DATABASE_CONFIG_ROUTE = "/databaseConfig"
+const val REFERENCE_GENOME_ROUTE = "/referenceGenome"
 
 @RestController
 @RequestMapping("/sample")
-class InfoController(private val siloQueryModel: SiloQueryModel) {
+class InfoController(
+    private val siloQueryModel: SiloQueryModel,
+    private val databaseConfig: DatabaseConfig,
+    private val referenceGenome: ReferenceGenome,
+) {
     @GetMapping(INFO_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
     @Operation(description = INFO_ENDPOINT_DESCRIPTION)
     fun getInfo(): LapisInfo {
         val siloInfo = siloQueryModel.getInfo()
         return LapisInfo(siloInfo.dataVersion)
     }
+
+    @GetMapping(DATABASE_CONFIG_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @Operation(description = DATABASE_CONFIG_ENDPOINT_DESCRIPTION)
+    fun getDatabaseConfig(): DatabaseConfig = databaseConfig
+
+    @GetMapping(REFERENCE_GENOME_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @Operation(description = REFERENCE_GENOME_ENDPOINT_DESCRIPTION)
+    fun getReferenceGenome(): ReferenceGenome = referenceGenome
 }

lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt

@@ -3,7 +3,7 @@ package org.genspectrum.lapis.controller
 import io.swagger.v3.oas.annotations.Parameter
 import io.swagger.v3.oas.annotations.media.Schema
 import org.genspectrum.lapis.config.REFERENCE_GENOME_SEGMENTS_APPLICATION_ARG_PREFIX
-import org.genspectrum.lapis.config.ReferenceGenome
+import org.genspectrum.lapis.config.ReferenceGenomeSchema
 import org.genspectrum.lapis.logging.RequestContext
 import org.genspectrum.lapis.model.SiloQueryModel
 import org.genspectrum.lapis.openApi.AminoAcidInsertions
@@ -41,7 +41,7 @@ const val IS_SINGLE_SEGMENT_SEQUENCE_EXPRESSION =
 class SingleSegmentedSequenceController(
     private val siloQueryModel: SiloQueryModel,
     private val requestContext: RequestContext,
-    private val referenceGenome: ReferenceGenome,
+    private val referenceGenomeSchema: ReferenceGenomeSchema,
 ) {
     @GetMapping(ALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE, produces = ["text/x-fasta"])
     @LapisAlignedSingleSegmentedNucleotideSequenceResponse
@@ -87,7 +87,7 @@ class SingleSegmentedSequenceController(
         return siloQueryModel.getGenomicSequence(
             request,
             SequenceType.ALIGNED,
-            referenceGenome.nucleotideSequences[0].name,
+            referenceGenomeSchema.nucleotideSequences[0].name,
         )
     }
 
@@ -103,7 +103,7 @@ class SingleSegmentedSequenceController(
         return siloQueryModel.getGenomicSequence(
             request,
             SequenceType.ALIGNED,
-            referenceGenome.nucleotideSequences[0].name,
+            referenceGenomeSchema.nucleotideSequences[0].name,
         )
     }
 }

lapis2/src/main/kotlin/org/genspectrum/lapis/model/SiloQueryModel.kt

@@ -1,6 +1,6 @@
 package org.genspectrum.lapis.model
 
-import org.genspectrum.lapis.config.ReferenceGenome
+import org.genspectrum.lapis.config.ReferenceGenomeSchema
 import org.genspectrum.lapis.request.MutationProportionsRequest
 import org.genspectrum.lapis.request.SequenceFiltersRequest
 import org.genspectrum.lapis.request.SequenceFiltersRequestWithFields
@@ -20,7 +20,7 @@ import org.springframework.stereotype.Component
 class SiloQueryModel(
     private val siloClient: SiloClient,
     private val siloFilterExpressionMapper: SiloFilterExpressionMapper,
-    private val referenceGenome: ReferenceGenome,
+    private val referenceGenomeSchema: ReferenceGenomeSchema,
 ) {
     fun getAggregated(sequenceFilters: SequenceFiltersRequestWithFields) =
         siloClient.sendQuery(
@@ -51,7 +51,7 @@ class SiloQueryModel(
         )
         return data.map { it ->
             val sequenceName =
-                if (referenceGenome.isSingleSegmented()) it.mutation else "${it.sequenceName}:${it.mutation}"
+                if (referenceGenomeSchema.isSingleSegmented()) it.mutation else "${it.sequenceName}:${it.mutation}"
 
             NucleotideMutationResponse(
                 sequenceName,
@@ -110,7 +110,7 @@ class SiloQueryModel(
         )
 
         return data.map { it ->
-            val sequenceName = if (referenceGenome.isSingleSegmented()) "" else "${it.sequenceName}:"
+            val sequenceName = if (referenceGenomeSchema.isSingleSegmented()) "" else "${it.sequenceName}:"
 
             NucleotideInsertionResponse(
                 "ins_${sequenceName}${it.position}:${it.insertions}",

lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt

@@ -16,7 +16,7 @@ import VariantQueryParser.OrContext
 import VariantQueryParser.PangolineageQueryContext
 import org.antlr.v4.runtime.RuleContext
 import org.antlr.v4.runtime.tree.ParseTreeListener
-import org.genspectrum.lapis.config.ReferenceGenome
+import org.genspectrum.lapis.config.ReferenceGenomeSchema
 import org.genspectrum.lapis.request.LAPIS_INSERTION_AMBIGUITY_SYMBOL
 import org.genspectrum.lapis.request.SILO_INSERTION_AMBIGUITY_SYMBOL
 import org.genspectrum.lapis.silo.AminoAcidInsertionContains
@@ -34,7 +34,9 @@ import org.genspectrum.lapis.silo.PangoLineageEquals
 import org.genspectrum.lapis.silo.SiloFilterExpression
 import org.genspectrum.lapis.silo.StringEquals
 
-class VariantQueryCustomListener(val referenceGenome: ReferenceGenome) : VariantQueryBaseListener(), ParseTreeListener {
+class VariantQueryCustomListener(val referenceGenomeSchema: ReferenceGenomeSchema) :
+    VariantQueryBaseListener(),
+    ParseTreeListener {
     private val expressionStack = ArrayDeque<SiloFilterExpression>()
 
     fun getVariantQueryExpression(): SiloFilterExpression {
@@ -110,7 +112,7 @@ class VariantQueryCustomListener(val referenceGenome: ReferenceGenome) : Variant
             return
         }
         val position = ctx.position().text.toInt()
-        val gene = referenceGenome.getGeneFromLowercaseName(ctx.gene().text.lowercase()).name
+        val gene = referenceGenomeSchema.getGeneFromLowercaseName(ctx.gene().text.lowercase()).name
 
         val expression = when (val aaSymbol = ctx.possiblyAmbiguousAaSymbol()) {
             null -> HasAminoAcidMutation(gene, position)
@@ -122,7 +124,7 @@ class VariantQueryCustomListener(val referenceGenome: ReferenceGenome) : Variant
 
     override fun enterAaInsertionQuery(ctx: AaInsertionQueryContext) {
         val value = ctx.aaInsertionSymbol().joinToString("", transform = ::mapInsertionSymbol)
-        val gene = referenceGenome.getGeneFromLowercaseName(ctx.gene().text.lowercase()).name
+        val gene = referenceGenomeSchema.getGeneFromLowercaseName(ctx.gene().text.lowercase()).name
 
         expressionStack.addLast(
             AminoAcidInsertionContains(

lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryFacade.kt

@@ -5,17 +5,17 @@ import VariantQueryParser
 import org.antlr.v4.runtime.CharStreams
 import org.antlr.v4.runtime.CommonTokenStream
 import org.antlr.v4.runtime.tree.ParseTreeWalker
-import org.genspectrum.lapis.config.ReferenceGenome
+import org.genspectrum.lapis.config.ReferenceGenomeSchema
 import org.genspectrum.lapis.silo.SiloFilterExpression
 import org.springframework.stereotype.Component
 
 @Component
-class VariantQueryFacade(val referenceGenome: ReferenceGenome) {
+class VariantQueryFacade(val referenceGenomeSchema: ReferenceGenomeSchema) {
     fun map(variantQuery: String): SiloFilterExpression {
         val lexer = VariantQueryLexer(CharStreams.fromString(variantQuery))
         val tokens = CommonTokenStream(lexer)
         val parser = VariantQueryParser(tokens)
-        val listener = VariantQueryCustomListener(referenceGenome)
+        val listener = VariantQueryCustomListener(referenceGenomeSchema)
 
         val walker = ParseTreeWalker()
         walker.walk(listener, parser.start())