feat: add info to lapis response

GenSpectrum · Dec 12, 2023 · afff4ae · afff4ae
1 parent d939f44
commit afff4ae
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Showing 13 changed files with 107 additions and 16 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisResponse.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisResponse.kt
@@ -1,7 +1,8 @@
 package org.genspectrum.lapis.controller
 
+import org.genspectrum.lapis.request.LapisInfo
 import org.springframework.http.ProblemDetail
 
-data class LapisResponse<Data>(val data: Data)
+data class LapisResponse<Data>(val data: Data, val info: LapisInfo = LapisInfo())
 
-data class LapisErrorResponse(val error: ProblemDetail)
+data class LapisErrorResponse(val error: ProblemDetail, val info: LapisInfo = LapisInfo())
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt
@@ -27,6 +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.NucleotideInsertion
 import org.genspectrum.lapis.request.NucleotideMutation
 import org.genspectrum.lapis.request.OrderByField
@@ -249,8 +250,23 @@ private fun lapisResponseSchema(dataSchema: Schema<Any>) =
     Schema<Any>().type("object").properties(
         mapOf(
             "data" to Schema<Any>().type("array").items(dataSchema),
+            "info" to infoResponseSchema(),
         ),
-    ).required(listOf("data"))
+    ).required(listOf("data", "info"))
+
+private fun infoResponseSchema() =
+    Schema<Any>().type("object")
+        .description("Information about LAPIS.")
+        .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"),
+            ),
+        ).required(listOf("dataVersion"))
 
 private fun metadataFieldSchemas(databaseConfig: DatabaseConfig) =
     databaseConfig.schema.metadata.associate { it.name to Schema<String>().type(mapToOpenApiType(it.type)) }

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/Schemas.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/Schemas.kt
@@ -59,6 +59,8 @@ const val FORMAT_SCHEMA = "DataFormat"
 const val FIELDS_TO_AGGREGATE_BY_SCHEMA = "FieldsToAggregateBy"
 const val DETAILS_FIELDS_SCHEMA = "DetailsFields"
 
+const val LAPIS_DATA_VERSION_DESCRIPTION = "The data version of data in SILO."
+
 @Target(AnnotationTarget.FUNCTION, AnnotationTarget.CLASS)
 @Retention(AnnotationRetention.RUNTIME)
 @Operation
@@ -68,7 +70,8 @@ const val DETAILS_FIELDS_SCHEMA = "DetailsFields"
     headers = [
         Header(
             name = LAPIS_DATA_VERSION_HEADER,
-            description = "A timestamp of when the data was last updated.",
+            description = "$LAPIS_DATA_VERSION_DESCRIPTION " +
+                "Same as the value returned in the info object in the response body.",
             schema = Schema(type = "string"),
         ),
     ],

diff --git a/.../genspectrum/lapis/request/DataVersion.kt → ...rg/genspectrum/lapis/request/LapisInfo.kt b/.../genspectrum/lapis/request/DataVersion.kt → ...rg/genspectrum/lapis/request/LapisInfo.kt
@@ -1,20 +1,17 @@
 package org.genspectrum.lapis.request
 
+import org.genspectrum.lapis.controller.LapisErrorResponse
+import org.genspectrum.lapis.controller.LapisResponse
+import org.genspectrum.lapis.silo.DataVersion
 import org.springframework.core.MethodParameter
 import org.springframework.http.MediaType
 import org.springframework.http.converter.HttpMessageConverter
 import org.springframework.http.server.ServerHttpRequest
 import org.springframework.http.server.ServerHttpResponse
-import org.springframework.stereotype.Component
 import org.springframework.web.bind.annotation.ControllerAdvice
-import org.springframework.web.context.annotation.RequestScope
 import org.springframework.web.servlet.mvc.method.annotation.ResponseBodyAdvice
 
-@Component
-@RequestScope
-class DataVersion {
-    var dataVersion: String? = null
-}
+data class LapisInfo(var dataVersion: String? = null)
 
 const val LAPIS_DATA_VERSION_HEADER = "Lapis-Data-Version"
 
@@ -29,6 +26,12 @@ class ResponseBodyAdviceDataVersion(private val dataVersion: DataVersion) : Resp
         response: ServerHttpResponse,
     ): Any? {
         response.headers.add(LAPIS_DATA_VERSION_HEADER, dataVersion.dataVersion)
+
+        when (body) {
+            is LapisResponse<*> -> return LapisResponse(body.data, LapisInfo(dataVersion.dataVersion))
+            is LapisErrorResponse -> return LapisErrorResponse(body.error, LapisInfo(dataVersion.dataVersion))
+        }
+
         return body
     }
 

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/DataVersion.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/DataVersion.kt
@@ -0,0 +1,8 @@
+package org.genspectrum.lapis.silo
+
+import org.springframework.stereotype.Component
+import org.springframework.web.context.annotation.RequestScope
+
+@Component
+@RequestScope
+data class DataVersion(var dataVersion: String? = null)
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloClient.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloClient.kt
@@ -3,7 +3,6 @@ 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.request.DataVersion
 import org.springframework.beans.factory.annotation.Value
 import org.springframework.http.HttpHeaders
 import org.springframework.http.HttpStatus

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/auth/ProtectedDataAuthorizationTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/auth/ProtectedDataAuthorizationTest.kt
@@ -6,6 +6,7 @@ import io.mockk.every
 import io.mockk.verify
 import org.genspectrum.lapis.controller.AGGREGATED_ROUTE
 import org.genspectrum.lapis.model.SiloQueryModel
+import org.genspectrum.lapis.request.LapisInfo
 import org.genspectrum.lapis.request.SequenceFiltersRequestWithFields
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
@@ -38,10 +39,17 @@ class ProtectedDataAuthorizationTest(
 
     private val validRoute = AGGREGATED_ROUTE
 
+    @MockkBean
+    lateinit var lapisInfo: LapisInfo
+
     @BeforeEach
     fun setUp() {
         every { siloQueryModelMock.getAggregated(any()) } returns emptyList()
 
+        every {
+            lapisInfo.dataVersion
+        } returns "1234"
+
         MockKAnnotations.init(this)
     }
 

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/ExceptionHandlerTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/ExceptionHandlerTest.kt
@@ -5,7 +5,9 @@ import io.mockk.MockKAnnotations
 import io.mockk.MockKMatcherScope
 import io.mockk.every
 import org.genspectrum.lapis.model.SiloNotImplementedError
+import org.genspectrum.lapis.request.LapisInfo
 import org.genspectrum.lapis.response.AggregationData
+import org.genspectrum.lapis.silo.DataVersion
 import org.genspectrum.lapis.silo.SiloException
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
@@ -26,17 +28,24 @@ class ExceptionHandlerTest(
     @MockkBean
     lateinit var lapisController: LapisController
 
+    @MockkBean
+    lateinit var dataVersion: DataVersion
+
     @BeforeEach
     fun setUp() {
         MockKAnnotations.init(this)
+
+        every {
+            dataVersion.dataVersion
+        } returns "1234"
     }
 
     private val validRoute = "/aggregated"
 
     private fun MockKMatcherScope.validControllerCall() =
         lapisController.aggregated(any(), any(), any(), any(), any(), any(), any())
 
-    private val validResponse = LapisResponse(emptyList<AggregationData>())
+    private val validResponse = LapisResponse(emptyList<AggregationData>(), LapisInfo())
 
     @Test
     fun `throw NOT_FOUND(404) when route is not found`() {
@@ -60,6 +69,9 @@ class ExceptionHandlerTest(
                         "error": {
                             "title": "Internal Server Error",
                             "detail": "SomeMessage"
+                         },
+                         "info": {
+                            "dataVersion": "1234"
                          }
                     }
                     """,
@@ -81,6 +93,9 @@ class ExceptionHandlerTest(
                         "error": {
                             "title": "SomeTitle",
                             "detail": "SomeMessage"
+                         },
+                         "info": {
+                            "dataVersion": "1234"
                          }
                     }
                     """,
@@ -102,6 +117,9 @@ class ExceptionHandlerTest(
                         "error": {
                             "title": "Bad Request",
                             "detail": "SomeMessage"
+                         },
+                         "info": {
+                            "dataVersion": "1234"
                          }
                     }
                     """,
@@ -123,6 +141,9 @@ class ExceptionHandlerTest(
                         "error": {
                             "title": "Not Implemented",
                             "detail": "SomeMessage"
+                         },
+                         "info": {
+                            "dataVersion": "1234"
                          }
                     }
                     """,

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerCommonFieldsTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerCommonFieldsTest.kt
@@ -5,12 +5,14 @@ import com.ninjasquad.springmockk.MockkBean
 import io.mockk.every
 import org.genspectrum.lapis.model.SiloQueryModel
 import org.genspectrum.lapis.request.AminoAcidInsertion
+import org.genspectrum.lapis.request.LapisInfo
 import org.genspectrum.lapis.request.NucleotideInsertion
 import org.genspectrum.lapis.request.Order
 import org.genspectrum.lapis.request.OrderByField
 import org.genspectrum.lapis.request.SequenceFiltersRequestWithFields
 import org.genspectrum.lapis.response.AggregationData
 import org.hamcrest.Matchers
+import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.params.ParameterizedTest
 import org.junit.jupiter.params.provider.Arguments
@@ -33,6 +35,16 @@ class LapisControllerCommonFieldsTest(
     @MockkBean
     lateinit var siloQueryModelMock: SiloQueryModel
 
+    @MockkBean
+    lateinit var lapisInfo: LapisInfo
+
+    @BeforeEach
+    fun setup() {
+        every {
+            lapisInfo.dataVersion
+        } returns "1234"
+    }
+
     @Test
     fun `GET aggregated with a single orderBy field`() {
         every {

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerCsvTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerCsvTest.kt
@@ -7,13 +7,15 @@ import com.fasterxml.jackson.databind.node.TextNode
 import com.ninjasquad.springmockk.MockkBean
 import io.mockk.every
 import org.genspectrum.lapis.model.SiloQueryModel
+import org.genspectrum.lapis.request.LapisInfo
 import org.genspectrum.lapis.request.SequenceFiltersRequestWithFields
 import org.genspectrum.lapis.response.AggregationData
 import org.genspectrum.lapis.response.AminoAcidInsertionResponse
 import org.genspectrum.lapis.response.AminoAcidMutationResponse
 import org.genspectrum.lapis.response.DetailsData
 import org.genspectrum.lapis.response.NucleotideInsertionResponse
 import org.genspectrum.lapis.response.NucleotideMutationResponse
+import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.params.ParameterizedTest
 import org.junit.jupiter.params.provider.Arguments
 import org.junit.jupiter.params.provider.MethodSource
@@ -37,6 +39,16 @@ class LapisControllerCsvTest(
     @MockkBean
     lateinit var siloQueryModelMock: SiloQueryModel
 
+    @MockkBean
+    lateinit var lapisInfo: LapisInfo
+
+    @BeforeEach
+    fun setup() {
+        every {
+            lapisInfo.dataVersion
+        } returns "1234"
+    }
+
     @ParameterizedTest(name = "GET {0} returns empty JSON")
     @MethodSource("getEndpoints")
     fun `GET returns empty json`(endpoint: String) {

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerTest.kt
@@ -5,7 +5,6 @@ import com.fasterxml.jackson.databind.node.TextNode
 import com.ninjasquad.springmockk.MockkBean
 import io.mockk.every
 import org.genspectrum.lapis.model.SiloQueryModel
-import org.genspectrum.lapis.request.DataVersion
 import org.genspectrum.lapis.request.MutationProportionsRequest
 import org.genspectrum.lapis.request.NucleotideMutation
 import org.genspectrum.lapis.request.SequenceFiltersRequest
@@ -16,6 +15,7 @@ import org.genspectrum.lapis.response.AminoAcidMutationResponse
 import org.genspectrum.lapis.response.DetailsData
 import org.genspectrum.lapis.response.NucleotideInsertionResponse
 import org.genspectrum.lapis.response.NucleotideMutationResponse
+import org.genspectrum.lapis.silo.DataVersion
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.params.ParameterizedTest
@@ -67,6 +67,7 @@ class LapisControllerTest(
             .andExpect(jsonPath("\$.data[0].country").value("Switzerland"))
             .andExpect(jsonPath("\$.data[0].age").value(42))
             .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+            .andExpect(jsonPath("\$.info.dataVersion").value(1234))
     }
 
     @Test
@@ -87,6 +88,7 @@ class LapisControllerTest(
             .andExpect(status().isOk)
             .andExpect(jsonPath("\$.data[0].count").value(0))
             .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+            .andExpect(jsonPath("\$.info.dataVersion").value(1234))
     }
 
     @Test
@@ -170,6 +172,7 @@ class LapisControllerTest(
             .andExpect(jsonPath("\$.data[0].proportion").value(0.5))
             .andExpect(jsonPath("\$.data[0].count").value(42))
             .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+            .andExpect(jsonPath("\$.info.dataVersion").value(1234))
     }
 
     @ParameterizedTest(name = "GET {0} with minProportion")
@@ -215,6 +218,7 @@ class LapisControllerTest(
             .andExpect(jsonPath("\$.data[0].proportion").value(0.5))
             .andExpect(jsonPath("\$.data[0].count").value(42))
             .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+            .andExpect(jsonPath("\$.info.dataVersion").value(1234))
     }
 
     @ParameterizedTest(name = "POST {0} with invalid minProportion returns bad request")
@@ -272,6 +276,7 @@ class LapisControllerTest(
             .andExpect(jsonPath("\$.data[0].insertion").value("the insertion"))
             .andExpect(jsonPath("\$.data[0].count").value(42))
             .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+            .andExpect(jsonPath("\$.info.dataVersion").value(1234))
     }
 
     @ParameterizedTest(name = "GET {0}")
@@ -286,6 +291,7 @@ class LapisControllerTest(
             .andExpect(jsonPath("\$.data[0].insertion").value("the insertion"))
             .andExpect(jsonPath("\$.data[0].count").value(42))
             .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+            .andExpect(jsonPath("\$.info.dataVersion").value(1234))
     }
 
     private fun setupInsertionMock(endpoint: String) {
@@ -335,6 +341,7 @@ class LapisControllerTest(
             .andExpect(jsonPath("\$.data[0].country").value("Switzerland"))
             .andExpect(jsonPath("\$.data[0].age").value(42))
             .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+            .andExpect(jsonPath("\$.info.dataVersion").value(1234))
     }
 
     @Test
@@ -369,6 +376,7 @@ class LapisControllerTest(
             .andExpect(jsonPath("\$.data[0].country").value("Switzerland"))
             .andExpect(jsonPath("\$.data[0].age").value(42))
             .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+            .andExpect(jsonPath("\$.info.dataVersion").value(1234))
     }
 
     @Test

diff --git a/.../src/test/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceControllerTest.kt b/.../src/test/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceControllerTest.kt
@@ -5,8 +5,8 @@ import io.mockk.every
 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.model.SiloQueryModel
-import org.genspectrum.lapis.request.DataVersion
 import org.genspectrum.lapis.request.SequenceFiltersRequest
+import org.genspectrum.lapis.silo.DataVersion
 import org.genspectrum.lapis.silo.SequenceType
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test

diff --git a/...src/test/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceControllerTest.kt b/...src/test/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceControllerTest.kt
@@ -5,8 +5,8 @@ import io.mockk.every
 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.model.SiloQueryModel
-import org.genspectrum.lapis.request.DataVersion
 import org.genspectrum.lapis.request.SequenceFiltersRequest
+import org.genspectrum.lapis.silo.DataVersion
 import org.genspectrum.lapis.silo.SequenceType
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test