diff --git a/.idea/runConfigurations/LapisV2Protected.xml b/.idea/runConfigurations/LapisV2Protected.xml
index e330b3600..4510b1bfb 100644
--- a/.idea/runConfigurations/LapisV2Protected.xml
+++ b/.idea/runConfigurations/LapisV2Protected.xml
@@ -1,7 +1,7 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="LapisV2Protected" type="SpringBootApplicationConfigurationType" factoryName="Spring Boot">
     <module name="lapis-v2.main" />
-    <option name="PROGRAM_PARAMETERS" value="--silo.url=http://localhost:8081 --lapis.databaseConfig.path=lapis2/src/test/resources/config/protectedDataDatabaseConfig.yaml --lapis.accessKeys.path=lapis2/src/test/resources/config/testAccessKeys.yaml --referenceGenomeFilename=siloLapisTests/testData/reference_genomes.json" />
+    <option name="PROGRAM_PARAMETERS" value="--silo.url=http://localhost:8081 --lapis.databaseConfig.path=siloLapisTests/testData/testDatabaseConfig.yaml --lapis.accessKeys.path=lapis2/src/test/resources/config/testAccessKeys.yaml --referenceGenomeFilename=siloLapisTests/testData/reference_genomes.json" />
     <option name="SPRING_BOOT_MAIN_CLASS" value="org.genspectrum.lapis.LapisApplicationKt" />
     <option name="WORKING_DIRECTORY" value="file://$PROJECT_DIR$" />
     <method v="2">
diff --git a/lapis2-docs/src/components/ConfigGenerator/AdditionalInformationWizard.tsx b/lapis2-docs/src/components/ConfigGenerator/AdditionalInformationWizard.tsx
index e7afdca6a..736ae44d2 100644
--- a/lapis2-docs/src/components/ConfigGenerator/AdditionalInformationWizard.tsx
+++ b/lapis2-docs/src/components/ConfigGenerator/AdditionalInformationWizard.tsx
@@ -1,5 +1,5 @@
 import { type ChangeEvent, type FC, useContext, useEffect, useMemo } from 'react';
-import { type Config, ConfigContext, type MetadataType } from './configContext.tsx';
+import { ConfigContext, type MetadataType, type Schema } from './configContext.tsx';
 import { sentenceCase } from 'change-case';
 
 export function AdditionalInformationWizard() {
@@ -21,7 +21,7 @@ const MetadataDropDown: FC<MetadataDropDownProps> = ({ name, filterByType }) =>
     const { config, modifyConfigField, removeConfigField } = useContext(ConfigContext);
 
     useEffect(() => {
-        function setInitialAdditionalInfo(additionalInfoName: keyof Config, additionalInfoType: string) {
+        function setInitialAdditionalInfo(additionalInfoName: keyof Schema, additionalInfoType: string) {
             const currentAdditionalInfo = config[additionalInfoName];
             let metadataOfAdditionalInfo;
 
diff --git a/lapis2-docs/src/components/ConfigGenerator/MetadataWizard.tsx b/lapis2-docs/src/components/ConfigGenerator/MetadataWizard.tsx
index cffb2db4c..58d8fd97f 100644
--- a/lapis2-docs/src/components/ConfigGenerator/MetadataWizard.tsx
+++ b/lapis2-docs/src/components/ConfigGenerator/MetadataWizard.tsx
@@ -105,7 +105,7 @@ export function MetadataEditModal({ index, metadata }: { index: number; metadata
 
     const [metadataType, setMetadataType] = useState<MetadataType>(metadata.type);
     const [metadataName, setMetadataName] = useState(metadata.name);
-    const [generateIndex, setGenerateIndex] = useState(metadata.generateIndex);
+    const [generateIndex, setGenerateIndex] = useState(!!metadata.generateIndex);
 
     const handleUpdateMetadata = () => {
         updateMetadata({ ...metadata, name: metadataName, type: metadataType, generateIndex }, index);
diff --git a/lapis2-docs/src/components/ConfigGenerator/UploadConfig.tsx b/lapis2-docs/src/components/ConfigGenerator/UploadConfig.tsx
index 359cd6986..4e54d5cbf 100644
--- a/lapis2-docs/src/components/ConfigGenerator/UploadConfig.tsx
+++ b/lapis2-docs/src/components/ConfigGenerator/UploadConfig.tsx
@@ -1,5 +1,5 @@
 import { type ChangeEvent, type Dispatch, type DragEvent, type SetStateAction, useState } from 'react';
-import { ConfigSchema, type PartialConfig } from './configContext.tsx';
+import { configSchema, type PartialConfig } from './configContext.tsx';
 import { load } from 'js-yaml';
 
 export type UploadConfigProps = {
@@ -16,9 +16,13 @@ export function UploadConfig({ setConfig }: UploadConfigProps) {
                 return;
             }
             const fileContent = fileReader.result.toString();
-            const config = ConfigSchema.parse(load(fileContent));
+            const config = configSchema.safeParse(load(fileContent));
 
-            setConfig(config);
+            if (config.success) {
+                setConfig(config.data.schema);
+            } else {
+                alert('Invalid config file: ' + config.error.message);
+            }
         };
         fileReader.readAsText(file);
     };
diff --git a/lapis2-docs/src/components/ConfigGenerator/configContext.tsx b/lapis2-docs/src/components/ConfigGenerator/configContext.tsx
index 6c0365fd4..296043bf0 100644
--- a/lapis2-docs/src/components/ConfigGenerator/configContext.tsx
+++ b/lapis2-docs/src/components/ConfigGenerator/configContext.tsx
@@ -24,49 +24,37 @@ export type MetadataType = z.infer<typeof metadataTypeSchema>;
 export const metadataSchema = z.object({
     name: z.string(),
     type: metadataTypeSchema,
-    generateIndex: z.boolean(),
+    generateIndex: z.boolean().optional(),
     autocomplete: z.boolean().optional(),
     required: z.boolean().optional(),
     notSearchable: z.boolean().optional(),
 });
 
-export type Metadata = {
-    name: string;
-    type: MetadataType;
-    generateIndex: boolean;
-    autocomplete?: boolean;
-    required?: boolean;
-    notSearchable?: boolean;
-};
+export type Metadata = z.infer<typeof metadataSchema>;
 
 export const featureSchema = z.object({
     name: z.string(),
 });
 export type Feature = z.infer<typeof featureSchema>;
 
-export const ConfigSchema = z.object({
+export const schemaSchema = z.object({
     instanceName: z.string(),
     opennessLevel: opennessLevelSchema,
     metadata: z.array(metadataSchema),
     primaryKey: z.string(),
     dateToSortBy: z.string(),
     partitionBy: z.string(),
-    tableColumns: z.array(z.string()),
+    tableColumns: z.array(z.string()).optional(),
     features: z.array(featureSchema),
 });
 
-export type Config = {
-    instanceName: string;
-    opennessLevel: OpennessLevel;
-    metadata: Metadata[];
-    primaryKey: string;
-    dateToSortBy: string;
-    partitionBy: string;
-    tableColumns: string[];
-    features: Feature[];
-};
+export type Schema = z.infer<typeof schemaSchema>;
+
+export const configSchema = z.object({
+    schema: schemaSchema,
+});
 
-export type PartialConfig = Partial<Config> & { metadata: Metadata[] };
+export type PartialConfig = Partial<Schema> & { metadata: Metadata[] };
 
 export type ConfigContextType = {
     configType: ConfigType;
@@ -78,8 +66,8 @@ export type ConfigContextType = {
     addNewTableColumn: (newColumnName: string) => void;
     updateTableColumn: (columnName: string, index: number) => void;
     deleteTableColumn: (index: number) => void;
-    modifyConfigField: <T extends keyof Config>(field: T, value: Config[T]) => void;
-    removeConfigField: (field: keyof Config) => void;
+    modifyConfigField: <T extends keyof Schema>(field: T, value: Schema[T]) => void;
+    removeConfigField: (field: keyof Schema) => void;
     modifyFeatureFields: (featureName: string, action: 'add' | 'delete') => void;
 };
 
@@ -166,11 +154,11 @@ export const ConfigProvider: FC<PropsWithChildren<{ initialConfig: PartialConfig
         });
     };
 
-    const modifyConfigField = <T extends keyof Config>(field: T, value: Config[T]) => {
+    const modifyConfigField = <T extends keyof Schema>(field: T, value: Schema[T]) => {
         setConfig({ ...config, [field]: value });
     };
 
-    const removeConfigField = (field: keyof Config) => {
+    const removeConfigField = (field: keyof Schema) => {
         delete config[field];
         setConfig({ ...config });
     };