feat: add info controller

GenSpectrum · Dec 12, 2023 · 78f9c69 · 78f9c69
1 parent 22e5f49
commit 78f9c69
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Showing 9 changed files with 117 additions and 20 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ControllerDescriptions.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ControllerDescriptions.kt
@@ -15,6 +15,7 @@ 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 ALIGNED_AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION =
     "Returns a string of fasta formated aligned amino acid sequences. Only sequences matching the specified " +

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/InfoController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/InfoController.kt
@@ -0,0 +1,20 @@
+package org.genspectrum.lapis.controller
+
+import io.swagger.v3.oas.annotations.Operation
+import org.genspectrum.lapis.model.SiloQueryModel
+import org.genspectrum.lapis.request.LapisInfo
+import org.springframework.http.MediaType
+import org.springframework.web.bind.annotation.GetMapping
+import org.springframework.web.bind.annotation.RestController
+
+const val INFO_ROUTE = "/info"
+
+@RestController
+class InfoController(private val siloQueryModel: SiloQueryModel) {
+    @GetMapping(INFO_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @Operation(description = INFO_ENDPOINT_DESCRIPTION)
+    fun getInfo(): LapisInfo {
+        val siloInfo = siloQueryModel.getInfo()
+        return LapisInfo(siloInfo.dataVersion)
+    }
+}
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/model/SiloQueryModel.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/model/SiloQueryModel.kt
@@ -7,6 +7,7 @@ import org.genspectrum.lapis.request.SequenceFiltersRequestWithFields
 import org.genspectrum.lapis.response.AminoAcidInsertionResponse
 import org.genspectrum.lapis.response.AminoAcidMutationResponse
 import org.genspectrum.lapis.response.DetailsData
+import org.genspectrum.lapis.response.InfoData
 import org.genspectrum.lapis.response.NucleotideInsertionResponse
 import org.genspectrum.lapis.response.NucleotideMutationResponse
 import org.genspectrum.lapis.silo.SequenceType
@@ -156,4 +157,6 @@ class SiloQueryModel(
             ),
         ).joinToString("\n") { ">${it.sequenceKey}\n${it.sequence}" }
     }
+
+    fun getInfo(): InfoData = siloClient.callInfo()
 }
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt
@@ -27,7 +27,7 @@ import org.genspectrum.lapis.controller.OFFSET_PROPERTY
 import org.genspectrum.lapis.controller.ORDER_BY_PROPERTY
 import org.genspectrum.lapis.request.AminoAcidInsertion
 import org.genspectrum.lapis.request.AminoAcidMutation
-import org.genspectrum.lapis.request.LAPIS_DATA_VERSION_HEADER
+import org.genspectrum.lapis.request.LapisInfo
 import org.genspectrum.lapis.request.NucleotideInsertion
 import org.genspectrum.lapis.request.NucleotideMutation
 import org.genspectrum.lapis.request.OrderByField
@@ -255,16 +255,13 @@ private fun lapisResponseSchema(dataSchema: Schema<Any>) =
     ).required(listOf("data", "info"))
 
 private fun infoResponseSchema() =
-    Schema<Any>().type("object")
-        .description("Information about LAPIS.")
+    Schema<LapisInfo>().type("object")
+        .description(LAPIS_INFO_DESCRIPTION)
         .properties(
             mapOf(
                 "dataVersion" to Schema<String>().type("string")
-                    .description(
-                        "$LAPIS_DATA_VERSION_DESCRIPTION " +
-                            "Same as the value of the header \"$LAPIS_DATA_VERSION_HEADER\".",
-                    )
-                    .example("1702305399"),
+                    .description(LAPIS_DATA_VERSION_RESPONSE_DESCRIPTION)
+                    .example(LAPIS_DATA_VERSION_EXAMPLE),
             ),
         ).required(listOf("dataVersion"))
 

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/Schemas.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/Schemas.kt
@@ -59,7 +59,13 @@ const val FORMAT_SCHEMA = "DataFormat"
 const val FIELDS_TO_AGGREGATE_BY_SCHEMA = "FieldsToAggregateBy"
 const val DETAILS_FIELDS_SCHEMA = "DetailsFields"
 
+const val LAPIS_INFO_DESCRIPTION = "Information about LAPIS."
+const val LAPIS_DATA_VERSION_EXAMPLE = "1702305399"
 const val LAPIS_DATA_VERSION_DESCRIPTION = "The data version of data in SILO."
+const val LAPIS_DATA_VERSION_HEADER_DESCRIPTION = "$LAPIS_DATA_VERSION_DESCRIPTION " +
+    "Same as the value returned in the info object in the response body."
+const val LAPIS_DATA_VERSION_RESPONSE_DESCRIPTION = "$LAPIS_DATA_VERSION_DESCRIPTION " +
+    "Same as the value returned in the info object in the header '$LAPIS_DATA_VERSION_HEADER'."
 
 @Target(AnnotationTarget.FUNCTION, AnnotationTarget.CLASS)
 @Retention(AnnotationRetention.RUNTIME)
@@ -70,8 +76,7 @@ const val LAPIS_DATA_VERSION_DESCRIPTION = "The data version of data in SILO."
     headers = [
         Header(
             name = LAPIS_DATA_VERSION_HEADER,
-            description = "$LAPIS_DATA_VERSION_DESCRIPTION " +
-                "Same as the value returned in the info object in the response body.",
+            description = LAPIS_DATA_VERSION_HEADER_DESCRIPTION,
             schema = Schema(type = "string"),
         ),
     ],

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/LapisInfo.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/LapisInfo.kt
@@ -1,7 +1,11 @@
 package org.genspectrum.lapis.request
 
+import io.swagger.v3.oas.annotations.media.Schema
 import org.genspectrum.lapis.controller.LapisErrorResponse
 import org.genspectrum.lapis.controller.LapisResponse
+import org.genspectrum.lapis.openApi.LAPIS_DATA_VERSION_EXAMPLE
+import org.genspectrum.lapis.openApi.LAPIS_DATA_VERSION_RESPONSE_DESCRIPTION
+import org.genspectrum.lapis.openApi.LAPIS_INFO_DESCRIPTION
 import org.genspectrum.lapis.silo.DataVersion
 import org.springframework.core.MethodParameter
 import org.springframework.http.MediaType
@@ -11,7 +15,13 @@ import org.springframework.http.server.ServerHttpResponse
 import org.springframework.web.bind.annotation.ControllerAdvice
 import org.springframework.web.servlet.mvc.method.annotation.ResponseBodyAdvice
 
-data class LapisInfo(var dataVersion: String? = null)
+@Schema(description = LAPIS_INFO_DESCRIPTION)
+data class LapisInfo(
+    @Schema(
+        description = LAPIS_DATA_VERSION_RESPONSE_DESCRIPTION,
+        example = LAPIS_DATA_VERSION_EXAMPLE,
+    ) var dataVersion: String? = null,
+)
 
 const val LAPIS_DATA_VERSION_HEADER = "Lapis-Data-Version"
 

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/response/SiloResponse.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/response/SiloResponse.kt
@@ -86,6 +86,10 @@ data class SequenceData(
     val sequence: String,
 )
 
+data class InfoData(
+    val dataVersion: String,
+)
+
 @JsonComponent
 class SequenceDataDeserializer(val databaseConfig: DatabaseConfig) : JsonDeserializer<SequenceData>() {
     override fun deserialize(

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloClient.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloClient.kt
@@ -3,6 +3,7 @@ package org.genspectrum.lapis.silo
 import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.module.kotlin.readValue
 import mu.KotlinLogging
+import org.genspectrum.lapis.response.InfoData
 import org.springframework.beans.factory.annotation.Value
 import org.springframework.http.HttpHeaders
 import org.springframework.http.HttpStatus
@@ -35,6 +36,20 @@ class SiloClient(
             .POST(HttpRequest.BodyPublishers.ofString(queryJson))
             .build()
 
+        val response = send(client, request)
+
+        try {
+            return objectMapper.readValue(response.body(), query.action.typeReference).queryResult
+        } catch (exception: Exception) {
+            val message = "Could not parse response from silo: " + exception::class.toString() + " " + exception.message
+            throw RuntimeException(message, exception)
+        }
+    }
+
+    private fun send(
+        client: HttpClient,
+        request: HttpRequest?,
+    ): HttpResponse<String> {
         val response = try {
             client.send(request, BodyHandlers.ofString())
         } catch (exception: Exception) {
@@ -70,18 +85,27 @@ class SiloClient(
             )
         }
 
-        addDataVersion(response)
+        addDataVersionToRequestScope(response)
+        return response
+    }
 
-        try {
-            return objectMapper.readValue(response.body(), query.action.typeReference).queryResult
-        } catch (exception: Exception) {
-            val message = "Could not parse response from silo: " + exception::class.toString() + " " + exception.message
-            throw RuntimeException(message, exception)
-        }
+    fun callInfo(): InfoData {
+        log.info { "Calling SILO info" }
+
+        val client = HttpClient.newHttpClient()
+        val request = HttpRequest.newBuilder(URI("$siloUrl/info")).GET().build()
+
+        val response = send(client, request)
+
+        return InfoData(getDataVersion(response))
+    }
+
+    private fun addDataVersionToRequestScope(response: HttpResponse<String>) {
+        dataVersion.dataVersion = getDataVersion(response)
     }
 
-    private fun addDataVersion(response: HttpResponse<String>) {
-        dataVersion.dataVersion = response.headers().firstValue("data-version").orElse("")
+    private fun getDataVersion(response: HttpResponse<String>): String {
+        return response.headers().firstValue("data-version").orElse("")
     }
 }
 

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/InfoControllerTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/InfoControllerTest.kt
@@ -0,0 +1,33 @@
+package org.genspectrum.lapis.controller
+
+import com.ninjasquad.springmockk.MockkBean
+import io.mockk.every
+import org.genspectrum.lapis.model.SiloQueryModel
+import org.genspectrum.lapis.response.InfoData
+import org.junit.jupiter.api.Test
+import org.springframework.beans.factory.annotation.Autowired
+import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
+import org.springframework.boot.test.context.SpringBootTest
+import org.springframework.test.web.servlet.MockMvc
+import org.springframework.test.web.servlet.request.MockMvcRequestBuilders
+import org.springframework.test.web.servlet.result.MockMvcResultMatchers
+
+@SpringBootTest
+@AutoConfigureMockMvc
+class InfoControllerTest(
+    @Autowired val mockMvc: MockMvc,
+) {
+    @MockkBean
+    lateinit var siloQueryModelMock: SiloQueryModel
+
+    @Test
+    fun `GET info`() {
+        every {
+            siloQueryModelMock.getInfo()
+        } returns InfoData("1234")
+
+        mockMvc.perform(MockMvcRequestBuilders.get(INFO_ROUTE))
+            .andExpect(MockMvcResultMatchers.status().isOk)
+            .andExpect(MockMvcResultMatchers.jsonPath("\$.dataVersion").value("1234"))
+    }
+}