fix(lapis): return proper error message when lineage definition from SILO is invalid YAML (#1117)

resolves #1104

Author: fengelniederhammer

lapis/src/main/kotlin/org/genspectrum/lapis/silo/SiloClient.kt

@@ -3,8 +3,8 @@ package org.genspectrum.lapis.silo
 import com.fasterxml.jackson.annotation.JsonInclude
 import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.module.kotlin.readValue
-import mu.KotlinLogging
 import org.genspectrum.lapis.controller.LapisHeaders.REQUEST_ID
+import org.genspectrum.lapis.log
 import org.genspectrum.lapis.logging.RequestContext
 import org.genspectrum.lapis.logging.RequestIdContext
 import org.genspectrum.lapis.response.InfoData
@@ -22,8 +22,6 @@ import java.net.http.HttpResponse
 import java.net.http.HttpResponse.BodyHandlers
 import java.util.stream.Stream
 
-private val log = KotlinLogging.logger {}
-
 @Component
 class SiloClient(
     private val cachedSiloClient: CachedSiloClient,
@@ -129,7 +127,20 @@ open class CachedSiloClient(
             tryToReadSiloErrorFromBody = ::tryToReadSiloErrorFromString,
         ) { it.GET() }
 
-        return yamlObjectMapper.objectMapper.readValue(response.body())
+        val body = response.body()
+        try {
+            return yamlObjectMapper.objectMapper.readValue(body)
+        } catch (e: Exception) {
+            log.error {
+                val truncateLength = 1000
+                val bodyToLog = when {
+                    body.length > truncateLength -> body.substring(0, truncateLength) + "... (truncated)"
+                    else -> body
+                }
+                "Failed to parse lineage definition from SILO, it was: '$bodyToLog'"
+            }
+            throw RuntimeException("Failed to parse lineage definition from SILO: ${e.message}", e)
+        }
     }
 
     private fun <ResponseBodyType> send(

lapis/src/test/kotlin/org/genspectrum/lapis/silo/SiloClientTest.kt

@@ -479,6 +479,26 @@ class SiloClientTest(
         )
     }
 
+    @Test
+    fun `GIVEN silo returns invalid lineage definition file THEN returns appropriate error`() {
+        val columnName = "test_column"
+        MockServerClient("localhost", MOCK_SERVER_PORT)
+            .`when`(
+                request()
+                    .withMethod("GET")
+                    .withPath("/lineageDefinition/$columnName")
+                    .withHeader("X-Request-Id", REQUEST_ID_VALUE),
+            )
+            .respond(
+                response()
+                    .withStatusCode(200)
+                    .withBody(""),
+            )
+
+        val exception = assertThrows<RuntimeException> { underTest.getLineageDefinition(columnName) }
+        assertThat(exception.message, containsString("Failed to parse lineage definition from SILO: "))
+    }
+
     companion object {
         @JvmStatic
         val mutationActions = listOf(