fix(model-server): deadlock caused by non-existing lock ordering

model-server/src/main/kotlin/org/modelix/model/server/handlers/HealthApiImpl.kt

@@ -25,9 +25,11 @@ class HealthApiImpl(
 
     private fun isHealthy(): Boolean {
         val store = stores.getGlobalStoreClient()
-        val value = toLong(store[HEALTH_KEY]) + 1
-        store.put(HEALTH_KEY, java.lang.Long.toString(value))
-        return toLong(store[HEALTH_KEY]) >= value
+        return store.getTransactionManager().runWrite {
+            val value = toLong(store[HEALTH_KEY]) + 1
+            store.put(HEALTH_KEY, java.lang.Long.toString(value))
+            toLong(store[HEALTH_KEY]) >= value
+        }
     }
 
     private fun toLong(value: String?): Long {

model-server/src/main/kotlin/org/modelix/model/server/handlers/IRepositoriesManager.kt

@@ -6,6 +6,7 @@ import org.modelix.model.lazy.CLVersion
 import org.modelix.model.lazy.IDeserializingKeyValueStore
 import org.modelix.model.lazy.RepositoryId
 import org.modelix.model.server.store.IStoreClient
+import org.modelix.model.server.store.ITransactionManager
 import org.modelix.model.server.store.StoreManager
 
 interface IRepositoriesManager {
@@ -18,25 +19,23 @@ interface IRepositoriesManager {
      * If the server ID was created previously but is only stored under a legacy database key,
      * it also gets stored under the current and all legacy database keys.
      */
-    suspend fun maybeInitAndGetSeverId(): String
+    fun maybeInitAndGetSeverId(): String
     fun getRepositories(): Set<RepositoryId>
-    suspend fun createRepository(repositoryId: RepositoryId, userName: String?, useRoleIds: Boolean = true, legacyGlobalStorage: Boolean = false): CLVersion
-    suspend fun removeRepository(repository: RepositoryId): Boolean
+    fun createRepository(repositoryId: RepositoryId, userName: String?, useRoleIds: Boolean = true, legacyGlobalStorage: Boolean = false): CLVersion
+    fun removeRepository(repository: RepositoryId): Boolean
 
     fun getBranches(repositoryId: RepositoryId): Set<BranchReference>
 
-    suspend fun removeBranches(repository: RepositoryId, branchNames: Set<String>)
-
     /**
      * Same as [removeBranches] but blocking.
      * Caller is expected to execute it outside the request thread.
      */
-    fun removeBranchesBlocking(repository: RepositoryId, branchNames: Set<String>)
-    suspend fun getVersion(branch: BranchReference): CLVersion?
-    suspend fun getVersion(repository: RepositoryId, versionHash: String): CLVersion?
-    suspend fun getVersionHash(branch: BranchReference): String?
+    fun removeBranches(repository: RepositoryId, branchNames: Set<String>)
+    fun getVersion(branch: BranchReference): CLVersion?
+    fun getVersion(repository: RepositoryId, versionHash: String): CLVersion?
+    fun getVersionHash(branch: BranchReference): String?
     suspend fun pollVersionHash(branch: BranchReference, lastKnown: String?): String
-    suspend fun mergeChanges(branch: BranchReference, newVersionHash: String): String
+    fun mergeChanges(branch: BranchReference, newVersionHash: String): String
 
     /**
      * Same as [mergeChanges] but blocking.
@@ -54,14 +53,15 @@ interface IRepositoriesManager {
     fun isIsolated(repository: RepositoryId): Boolean?
 
     fun getStoreManager(): StoreManager
+    fun getTransactionManager(): ITransactionManager
 }
 
 fun IRepositoriesManager.getBranchNames(repositoryId: RepositoryId): Set<String> {
     return getBranches(repositoryId).map { it.branchName }.toSet()
 }
 
-fun IRepositoriesManager.getStoreClient(repository: RepositoryId?): IStoreClient {
-    return getStoreManager().getStoreClient(repository?.takeIf { isIsolated(it) ?: false })
+fun IRepositoriesManager.getStoreClient(repository: RepositoryId?, immutable: Boolean): IStoreClient {
+    return getStoreManager().getStoreClient(repository?.takeIf { isIsolated(it) ?: false }, immutable)
 }
 
 fun IRepositoriesManager.getAsyncStore(repository: RepositoryId?): IAsyncObjectStore {

model-server/src/main/kotlin/org/modelix/model/server/handlers/KeyValueLikeModelServer.kt

@@ -13,7 +13,6 @@ import io.ktor.server.resources.put
 import io.ktor.server.response.respondText
 import io.ktor.server.routing.routing
 import io.ktor.util.pipeline.PipelineContext
-import kotlinx.coroutines.runBlocking
 import kotlinx.html.br
 import kotlinx.html.div
 import kotlinx.html.h1
@@ -34,7 +33,8 @@ import org.modelix.model.server.ModelServerPermissionSchema
 import org.modelix.model.server.store.ObjectInRepository
 import org.modelix.model.server.store.StoreManager
 import org.modelix.model.server.store.pollEntry
-import org.modelix.model.server.store.runTransactionSuspendable
+import org.modelix.model.server.store.runReadIO
+import org.modelix.model.server.store.runWriteIO
 import org.modelix.model.server.templates.PageWithMenuBar
 import java.io.IOException
 import java.util.*
@@ -67,7 +67,7 @@ class KeyValueLikeModelServer(
         // request to initialize it lazily, would make the code less robust.
         // Each change in the logic of RepositoriesManager#maybeInitAndGetSeverId would need
         // the special conditions in the affected requests to be updated.
-        runBlocking { repositoriesManager.maybeInitAndGetSeverId() }
+        repositoriesManager.getTransactionManager().runWrite { repositoriesManager.maybeInitAndGetSeverId() }
         application.apply {
             modelServerModule()
         }
@@ -95,7 +95,7 @@ class KeyValueLikeModelServer(
                 get<Paths.getKeyGet> {
                     val key = call.parameters["key"]!!
                     checkKeyPermission(key, EPermissionType.READ)
-                    val value = stores.getGlobalKeyValueStore()[key]
+                    val value = runRead { stores.getGlobalStoreClient()[key] }
                     respondValue(key, value)
                 }
                 get<Paths.pollKeyGet> {
@@ -112,21 +112,23 @@ class KeyValueLikeModelServer(
                 post<Paths.counterKeyPost> {
                     val key = call.parameters["key"]!!
                     checkKeyPermission(key, EPermissionType.WRITE)
-                    val value = stores.getGlobalStoreClient().generateId(key)
+                    val value = stores.getGlobalStoreClient(false).generateId(key)
                     call.respondText(text = value.toString())
                 }
 
                 get<Paths.getRecursivelyKeyGet> {
                     val key = call.parameters["key"]!!
                     checkKeyPermission(key, EPermissionType.READ)
-                    call.respondText(collect(key, this).toString(2), contentType = ContentType.Application.Json)
+                    call.respondText(runRead { collect(key, this) }.toString(2), contentType = ContentType.Application.Json)
                 }
 
                 put<Paths.putKeyPut> {
                     val key = call.parameters["key"]!!
                     val value = call.receiveText()
                     try {
-                        putEntries(mapOf(key to value))
+                        runWrite {
+                            putEntries(mapOf(key to value))
+                        }
                         call.respondText("OK")
                     } catch (e: NotFoundException) {
                         throw HttpException(HttpStatusCode.NotFound, title = "Not found", details = e.message, cause = e)
@@ -145,7 +147,9 @@ class KeyValueLikeModelServer(
                     }
                     entries = sortByDependency(entries)
                     try {
-                        putEntries(entries)
+                        runWrite {
+                            putEntries(entries)
+                        }
                         call.respondText(entries.size.toString() + " entries written")
                     } catch (e: NotFoundException) {
                         throw HttpException(HttpStatusCode.NotFound, title = "Not found", details = e.message, cause = e)
@@ -164,7 +168,7 @@ class KeyValueLikeModelServer(
                         checkKeyPermission(key, EPermissionType.READ)
                         keys.add(key)
                     }
-                    val values = stores.getGlobalStoreClient().getAll(keys)
+                    val values = runRead { stores.getGlobalStoreClient(false).getAll(keys) }
                     for (i in keys.indices) {
                         val respEntry = JSONObject()
                         respEntry.put("key", keys[i])
@@ -216,7 +220,7 @@ class KeyValueLikeModelServer(
             if (callContext != null) {
                 keys.forEach { callContext.checkKeyPermission(it, EPermissionType.READ) }
             }
-            val values = stores.getGlobalStoreClient().getAll(keys)
+            val values = stores.getGlobalStoreClient(false).getAll(keys)
             for (i in keys.indices) {
                 val key = keys[i]
                 val value = values[i]
@@ -246,7 +250,7 @@ class KeyValueLikeModelServer(
         return result
     }
 
-    private suspend fun CallContext.putEntries(newEntries: Map<String, String?>) {
+    private fun CallContext.putEntries(newEntries: Map<String, String?>) {
         val referencedKeys: MutableSet<String> = HashSet()
         for ((key, value) in newEntries) {
             checkKeyPermission(key, EPermissionType.WRITE)
@@ -303,17 +307,15 @@ class KeyValueLikeModelServer(
             // We could try to move the objects later, but since this API is deprecated, it's not worth the effort.
         }
 
-        stores.getGlobalStoreClient().runTransactionSuspendable {
-            stores.genericStore.putAll(hashedObjects.mapKeys { ObjectInRepository.global(it.key) })
-            stores.genericStore.putAll(userDefinedEntries.mapKeys { ObjectInRepository.global(it.key) })
-            for ((branch, value) in branchChanges) {
-                if (value == null) {
-                    checkPermission(ModelServerPermissionSchema.branch(branch).delete)
-                    repositoriesManager.removeBranchesBlocking(branch.repositoryId, setOf(branch.branchName))
-                } else {
-                    checkPermission(ModelServerPermissionSchema.branch(branch).push)
-                    repositoriesManager.mergeChangesBlocking(branch, value)
-                }
+        stores.genericStore.putAll(hashedObjects.mapKeys { ObjectInRepository.global(it.key) })
+        stores.genericStore.putAll(userDefinedEntries.mapKeys { ObjectInRepository.global(it.key) })
+        for ((branch, value) in branchChanges) {
+            if (value == null) {
+                checkPermission(ModelServerPermissionSchema.branch(branch).delete)
+                repositoriesManager.removeBranches(branch.repositoryId, setOf(branch.branchName))
+            } else {
+                checkPermission(ModelServerPermissionSchema.branch(branch).push)
+                repositoriesManager.mergeChangesBlocking(branch, value)
             }
         }
     }
@@ -363,4 +365,12 @@ class KeyValueLikeModelServer(
             else -> unknown()
         }
     }
+
+    private suspend fun <R> runRead(body: () -> R): R {
+        return repositoriesManager.getTransactionManager().runReadIO(body)
+    }
+
+    private suspend fun <R> runWrite(body: () -> R): R {
+        return repositoriesManager.getTransactionManager().runWriteIO(body)
+    }
 }

model-server/src/main/kotlin/org/modelix/model/server/handlers/ModelReplicationServer.kt

@@ -49,6 +49,8 @@ import org.modelix.model.server.api.v2.VersionDelta
 import org.modelix.model.server.api.v2.VersionDeltaStream
 import org.modelix.model.server.api.v2.VersionDeltaStreamV2
 import org.modelix.model.server.store.StoreManager
+import org.modelix.model.server.store.runReadIO
+import org.modelix.model.server.store.runWriteIO
 import org.modelix.modelql.core.IMemoizationPersistence
 import org.modelix.modelql.core.IStepOutput
 import org.modelix.modelql.core.MonoUnboundQuery
@@ -89,16 +91,15 @@ class ModelReplicationServer(
 
     override suspend fun PipelineContext<Unit, ApplicationCall>.getRepositories() {
         call.respondText(
-            repositoriesManager.getRepositories()
+            runRead { repositoriesManager.getRepositories() }
                 .filter { call.hasPermission(ModelServerPermissionSchema.repository(it).list) }
                 .joinToString("\n") { it.id },
         )
     }
 
     override suspend fun PipelineContext<Unit, ApplicationCall>.getRepositoryBranches(repository: String) {
         call.respondText(
-            repositoriesManager
-                .getBranchNames(repositoryId(repository))
+            runRead { repositoriesManager.getBranchNames(repositoryId(repository)) }
                 .filter { call.hasPermission(ModelServerPermissionSchema.repository(repository).branch(it).list) }
                 .joinToString("\n"),
         )
@@ -111,7 +112,9 @@ class ModelReplicationServer(
     ) {
         checkPermission(ModelServerPermissionSchema.repository(repository).branch(branch).pull)
         val branchRef = repositoryId(repository).getBranchReference(branch)
-        val versionHash = repositoriesManager.getVersionHash(branchRef) ?: throw BranchNotFoundException(branchRef)
+        val versionHash = runRead {
+            repositoriesManager.getVersionHash(branchRef) ?: throw BranchNotFoundException(branchRef)
+        }
         call.respondDelta(RepositoryId(repository), versionHash, lastKnown)
     }
 
@@ -122,7 +125,7 @@ class ModelReplicationServer(
     ) {
         checkPermission(ModelServerPermissionSchema.repository(repository).branch(branch).pull)
         val branchRef = repositoryId(repository).getBranchReference(branch)
-        val versionHash = repositoriesManager.getVersionHash(branchRef) ?: throw BranchNotFoundException(branchRef)
+        val versionHash = runRead { repositoriesManager.getVersionHash(branchRef) ?: throw BranchNotFoundException(branchRef) }
         call.respond(BranchV1(branch, versionHash))
     }
 
@@ -138,11 +141,13 @@ class ModelReplicationServer(
 
         checkPermission(ModelServerPermissionSchema.repository(repositoryId).branch(branch).delete)
 
-        if (!repositoriesManager.getBranchNames(repositoryId).contains(branch)) {
-            throw BranchNotFoundException(branch, repositoryId.id)
-        }
+        runWrite {
+            if (!repositoriesManager.getBranchNames(repositoryId).contains(branch)) {
+                throw BranchNotFoundException(branch, repositoryId.id)
+            }
 
-        repositoriesManager.removeBranches(repositoryId, setOf(branch))
+            repositoriesManager.removeBranches(repositoryId, setOf(branch))
+        }
 
         call.respond(HttpStatusCode.NoContent)
     }
@@ -153,7 +158,7 @@ class ModelReplicationServer(
     ) {
         checkPermission(ModelServerPermissionSchema.repository(repository).branch(branch).pull)
         val branchRef = repositoryId(repository).getBranchReference(branch)
-        val versionHash = repositoriesManager.getVersionHash(branchRef) ?: throw BranchNotFoundException(branchRef)
+        val versionHash = runRead { repositoriesManager.getVersionHash(branchRef) ?: throw BranchNotFoundException(branchRef) }
         call.respondText(versionHash)
     }
 
@@ -163,19 +168,23 @@ class ModelReplicationServer(
         legacyGlobalStorage: Boolean?,
     ) {
         checkPermission(ModelServerPermissionSchema.repository(repository).create)
-        val initialVersion = repositoriesManager.createRepository(
-            repositoryId(repository),
-            call.getUserName(),
-            useRoleIds ?: true,
-            legacyGlobalStorage ?: false,
-        )
+        val initialVersion = runWrite {
+            repositoriesManager.createRepository(
+                repositoryId(repository),
+                call.getUserName(),
+                useRoleIds ?: true,
+                legacyGlobalStorage ?: false,
+            )
+        }
         call.respondDelta(RepositoryId(repository), initialVersion.getContentHash(), null)
     }
 
     override suspend fun PipelineContext<Unit, ApplicationCall>.deleteRepository(repository: String) {
         checkPermission(ModelServerPermissionSchema.repository(repository).delete)
 
-        val foundAndDeleted = repositoriesManager.removeRepository(repositoryId(repository))
+        val foundAndDeleted = runWrite {
+            repositoriesManager.removeRepository(repositoryId(repository))
+        }
         if (foundAndDeleted) {
             call.respond(HttpStatusCode.NoContent)
         } else {
@@ -191,8 +200,10 @@ class ModelReplicationServer(
         val branchRef = repositoryId(repository).getBranchReference(branch)
         val deltaFromClient = call.receive<VersionDelta>()
         deltaFromClient.checkObjectHashes()
-        repositoriesManager.getStoreClient(RepositoryId(repository)).putAll(deltaFromClient.getAllObjects())
-        val mergedHash = repositoriesManager.mergeChanges(branchRef, deltaFromClient.versionHash)
+        repositoriesManager.getStoreClient(RepositoryId(repository), true).putAll(deltaFromClient.getAllObjects())
+        val mergedHash = runWrite {
+            repositoriesManager.mergeChanges(branchRef, deltaFromClient.versionHash)
+        }
         call.respondDelta(RepositoryId(repository), mergedHash, deltaFromClient.versionHash)
     }
 
@@ -217,7 +228,7 @@ class ModelReplicationServer(
         }
 
         val objects = withContext(Dispatchers.IO) {
-            repositoriesManager.getStoreClient(RepositoryId(repository)).getAll(keys)
+            repositoriesManager.getStoreClient(RepositoryId(repository), true).getAll(keys)
         }
 
         for (entry in objects) {
@@ -260,7 +271,7 @@ class ModelReplicationServer(
     ) {
         val branchRef = repositoryId(repository).getBranchReference(branchName)
         checkPermission(ModelServerPermissionSchema.branch(branchRef).query)
-        val version = repositoriesManager.getVersion(branchRef) ?: throw BranchNotFoundException(branchRef)
+        val version = runRead { repositoriesManager.getVersion(branchRef) ?: throw BranchNotFoundException(branchRef) }
         LOG.trace("Running query on {} @ {}", branchRef, version)
         val initialTree = version.getTree()
 
@@ -290,7 +301,9 @@ class ModelReplicationServer(
                             baseVersion = version,
                             operations = ops.map { it.getOriginalOp() }.toTypedArray(),
                         )
-                        repositoriesManager.mergeChanges(branchRef, newVersion.getContentHash())
+                        runWrite {
+                            repositoriesManager.mergeChanges(branchRef, newVersion.getContentHash())
+                        }
                     }
                 }
             })
@@ -330,7 +343,7 @@ class ModelReplicationServer(
         }
 
         withContext(Dispatchers.IO) {
-            repositoriesManager.getStoreClient(RepositoryId(repository)).putAll(entries, true)
+            repositoriesManager.getStoreClient(RepositoryId(repository), true).putAll(entries, true)
         }
         call.respondText("${entries.size} objects received")
     }
@@ -341,7 +354,7 @@ class ModelReplicationServer(
         lastKnown: String?,
     ) {
         checkPermission(ModelServerPermissionSchema.legacyGlobalObjects.read)
-        if (stores.getGlobalStoreClient()[versionHash] == null) {
+        if (runRead { stores.getGlobalStoreClient()[versionHash] } == null) {
             throw VersionNotFoundException(versionHash)
         }
         call.respondDelta(null, versionHash, lastKnown)
@@ -402,6 +415,14 @@ class ModelReplicationServer(
             }
         }
     }
+
+    private suspend fun <R> runRead(body: () -> R): R {
+        return repositoriesManager.getTransactionManager().runReadIO(body)
+    }
+
+    private suspend fun <R> runWrite(body: () -> R): R {
+        return repositoriesManager.getTransactionManager().runWriteIO(body)
+    }
 }
 
 /**