Fix compilation warnings from Ktor 3 / Kotlin 2.3.20 upgrade

- ArtifactStoreRead: readBytes() -> readRawBytes() (deprecated rename)
- Authentication: suppress Principal deprecation warning
- LinkedDataPlatform: suppress Route.intercept deprecation
- Protocol: remove redundant 'out' projection on beforeEach
- SparqlBuilder: suppress unchecked cast, fix always-true null check
  on non-nullable userId, remove unnecessary elvis operator

Co-Authored-By: doris.t.lam <dlamoris@gmail.com>

Author: devin-ai-integration[bot]

src/main/kotlin/org/openmbee/flexo/mms/SparqlBuilder.kt

@@ -101,6 +101,7 @@ fun serializePairs(node: Resource): String {
 abstract class SparqlBuilder<out Instance: SparqlBuilder<Instance>>(private val indentLevel: Int=1) {
     protected val sparqlString = StringBuilder()
 
+    @Suppress("UNCHECKED_CAST")
     fun raw(vararg sparql: String): Instance {
         sparqlString.append(sparql.joinToString("\n") { it.trimIndent()+"\n" })
 
@@ -309,7 +310,7 @@ class InsertBuilder(
 
     fun subtxn(subTxnId: String, extras: Map<String, String>?=null, setup: (TxnBuilder.() -> Unit)?=null): InsertBuilder {
         val properties = extras?.toMutableMap()?: mutableMapOf()
-        if(null != layer1.userId) properties["mms:user"] = "mu:"
+        properties["mms:user"] = "mu:"
         if(null != layer1.orgId) properties["mms:org"] = "mo:"
         if(null != layer1.repoId) properties["mms:repo"] = "mor:"
         if(null != layer1.branchId) properties["mms:branch"] = "morb:"
@@ -550,7 +551,7 @@ class UpdateBuilder(
             // prefixes(mms.prefixes)
 
             literal(
-                "_userId" to (layer1.userId?: ""),
+                "_userId" to layer1.userId,
                 "_orgId" to (layer1.orgId?: ""),
                 "_repoId" to (layer1.repoId?: ""),
                 "_branchId" to (layer1.branchId?: ""),

src/main/kotlin/org/openmbee/flexo/mms/routes/store/ArtifactStoreRead.kt

@@ -86,7 +86,7 @@ suspend fun <TRequestContext: GenericRequest> Layer1Context<TRequestContext, Sto
                     }
                 }
             }
-            val bytes = response.readBytes()
+            val bytes = response.readRawBytes()
             DecodedArtifact(contentType, bodyBinary = bytes)
         }
         else -> {

src/main/kotlin/org/openmbee/flexo/mms/server/Authentication.kt

@@ -32,4 +32,5 @@ fun Application.configureAuthentication() {
     }
 }
 
+@Suppress("DEPRECATION")
 data class UserDetailsPrincipal(val name: String, val groups: List<String>) : Principal

src/main/kotlin/org/openmbee/flexo/mms/server/LinkedDataPlatform.kt

@@ -154,6 +154,7 @@ fun Route.linkedDataPlatformResource(
     // scope all contained routes to specified (sub)path
     route(path) {
         // 4.2.1.6: all responses must contain the Link header
+        @Suppress("DEPRECATION")
         intercept(ApplicationCallPipeline.Call) {
             // response headers have not yet been sent
             if(!call.response.isCommitted) {

src/main/kotlin/org/openmbee/flexo/mms/server/Protocol.kt

@@ -103,7 +103,7 @@ abstract class GenericProtocolRoute<TRequestContext: GenericRequest>(
     /**
      * Set a callback to execute before each call handled under given route
      */
-    var beforeEach: (suspend Layer1Context<TRequestContext, out GenericResponse>.() -> Unit)? = null
+    var beforeEach: (suspend Layer1Context<TRequestContext, GenericResponse>.() -> Unit)? = null
 
     /**
      * Set default regex used to assert the slug is a legal identifier when POST-ing to create new resource