@noatgnu/cupcake-vanilla 1.3.13 → 1.3.15

package/{index.d.ts → types/noatgnu-cupcake-vanilla.d.ts}

@@ -1,7 +1,7 @@
 import * as _angular_core from '@angular/core';
-import { OnInit, EventEmitter, OnDestroy, ElementRef } from '@angular/core';
+import { OnInit, EventEmitter, OnChanges, SimpleChanges, OnDestroy, ElementRef, AfterViewInit, Renderer2 } from '@angular/core';
 import { Observable, OperatorFunction } from 'rxjs';
-import { BaseApiService, WebSocketService, AuthService, WebSocketMessage, NotificationService as NotificationService$1, ToastService, AsyncTaskQueryParams, PaginatedResponse as PaginatedResponse$1, AsyncTaskStatus, DownloadUrlResponse, MetadataExportRequest, AsyncTaskCreateResponse, BulkExportRequest, BulkExcelExportRequest, MetadataImportRequest, ValidationSchema, MetadataValidationRequest, ChunkedImportRequest, User, LabGroupService, LabGroup, MetadataValidationConfig, TaskType, TaskStatus, LabGroupQueryResponse, ResourceVisibility } from '@noatgnu/cupcake-core';
+import { BaseApiService, NotificationService as NotificationService$1, AsyncTaskQueryParams, PaginatedResponse as PaginatedResponse$1, AsyncTaskStatus, DownloadUrlResponse, MetadataExportRequest, AsyncTaskCreateResponse, BulkExportRequest, BulkExcelExportRequest, MetadataImportRequest, ValidationSchema, MetadataValidationRequest, SdrfFileValidationRequest, ChunkedImportRequest, WebSocketService, WebSocketMessage, DesktopRuntime, User, AuthService, LabGroupService, LabGroup, MetadataValidationConfig, TaskType, TaskStatus, LabGroupQueryResponse, ToastService, ResourceVisibility } from '@noatgnu/cupcake-core';
 export { WebSocketMessage } from '@noatgnu/cupcake-core';
 import * as _angular_forms from '@angular/forms';
 import { FormGroup, FormBuilder } from '@angular/forms';
@@ -19,9 +19,15 @@ interface PaginatedResponse<T> {
     previous?: string;
     results: T[];
 }
-interface ApiResponse<T = any> {
+interface ApiError {
+    message?: string;
+    code?: string;
+    details?: Record<string, string[]>;
+    [key: string]: unknown;
+}
+interface ApiResponse<T = unknown> {
     data?: T;
-    error?: any;
+    error?: ApiError;
     status: number;
     success: boolean;
 }
@@ -49,7 +55,9 @@ declare enum OntologyType {
     CHEBI = "chebi",
     CELL_ONTOLOGY = "cell_ontology",
     MS_UNIQUE_VOCABULARIES = "ms_unique_vocabularies",
-    PSI_MS = "psi_ms"
+    PSI_MS = "psi_ms",
+    BTO = "bto",
+    DOID = "doid"
 }
 declare const OntologyTypeLabels: Record<OntologyType, string>;
 declare enum TemplatePermissionLevel {
@@ -66,6 +74,125 @@ declare enum ColumnType {
     SPECIAL = "special"
 }
 
+type ColumnInputType = 'text' | 'select' | 'number_with_unit' | 'pattern' | 'ontology' | 'semver' | 'accession' | 'identifier';
+interface ColumnValidator {
+    type: string;
+    params: {
+        values?: string[];
+        units?: string[];
+        pattern?: string;
+        ontologies?: string[];
+        examples?: (string | number)[];
+        description?: string;
+        error_level?: string;
+        format?: string;
+        special_values?: string[];
+        [key: string]: unknown;
+    };
+}
+interface MetadataColumnTemplate extends BaseTimestampedModel {
+    id: number;
+    name: string;
+    description?: string;
+    columnName: string;
+    columnType: string;
+    defaultValue?: string;
+    defaultPosition?: number;
+    ontologyType?: string;
+    customOntologyFilters?: any;
+    enableTypeahead: boolean;
+    notApplicable: boolean;
+    notAvailable: boolean;
+    excelValidation?: any;
+    customValidationRules?: any;
+    apiEnhancements?: any;
+    visibility: string;
+    owner?: number;
+    ownerUsername?: string;
+    labGroup?: number;
+    labGroupName?: string;
+    schema?: number;
+    schemaName?: string;
+    sourceSchema?: string;
+    isSystemTemplate: boolean;
+    isActive: boolean;
+    usageCount?: number;
+    tags?: string[];
+    category?: string;
+    lastUsedAt?: string;
+    canEdit?: boolean;
+    canDelete?: boolean;
+    validators?: ColumnValidator[];
+    inputType?: ColumnInputType;
+    units?: string[];
+    possibleDefaultValues?: (string | number)[];
+    ontologyOptions?: string[];
+    baseColumn?: boolean;
+}
+interface MetadataColumnTemplateShare extends BaseTimestampedModel {
+    id: number;
+    template: number;
+    templateName?: string;
+    sharedWith: number;
+    sharedWithUsername?: string;
+    sharedBy: number;
+    sharedByUsername?: string;
+    canEdit: boolean;
+}
+interface MetadataColumnTemplateCreateRequest {
+    name: string;
+    description?: string;
+    columnName: string;
+    columnType: string;
+    defaultValue?: string;
+    defaultPosition?: number;
+    ontologyType?: string;
+    customOntologyFilters?: any;
+    enableTypeahead?: boolean;
+    notApplicable?: boolean;
+    notAvailable?: boolean;
+    excelValidation?: any;
+    customValidationRules?: any;
+    apiEnhancements?: any;
+    visibility?: string;
+    labGroup?: number;
+    tags?: string[];
+    category?: string;
+}
+interface MetadataColumnTemplateUpdateRequest {
+    name?: string;
+    description?: string;
+    columnName?: string;
+    columnType?: string;
+    defaultValue?: string;
+    defaultPosition?: number;
+    ontologyType?: string;
+    customOntologyFilters?: any;
+    enableTypeahead?: boolean;
+    notApplicable?: boolean;
+    notAvailable?: boolean;
+    excelValidation?: any;
+    customValidationRules?: any;
+    apiEnhancements?: any;
+    visibility?: string;
+    isActive?: boolean;
+    tags?: string[];
+    category?: string;
+}
+interface MetadataColumnTemplateShareCreateRequest {
+    template: number;
+    sharedWith: number;
+    canEdit?: boolean;
+}
+interface GroupedColumnTemplate {
+    columnName: string;
+    columnType: string;
+    schemaCount: number;
+    schemas: string[];
+    templateIds: number[];
+    sampleTemplate?: MetadataColumnTemplate;
+}
+
 interface MetadataColumnModifier {
     samples: string;
     value: string;
@@ -96,6 +223,12 @@ interface MetadataColumn extends BaseTimestampedModel {
     possibleDefaultValues: any[];
     staffOnly: boolean;
 }
+/**
+ * A synthetic MetadataColumn with id=0 derived from a template, used for ontology search
+ * in sheet mode where no backend table is loaded. id=0 is falsy so column-specific
+ * endpoints are not used; only the ontologyType and customOntologyFilters matter.
+ */
+declare function createSyntheticColumnFromTemplate(header: string, template: MetadataColumnTemplate): MetadataColumn;
 interface MetadataColumnCreateRequest {
     metadataTable: number;
     template?: number;
@@ -314,94 +447,72 @@ interface AdvancedAutofillResponse {
     variationsCombinations: number;
     strategy: string;
 }
-
-interface MetadataColumnTemplate extends BaseTimestampedModel {
-    id: number;
-    name: string;
-    description?: string;
-    columnName: string;
-    columnType: string;
-    defaultValue?: string;
-    defaultPosition?: number;
-    ontologyType?: string;
-    customOntologyFilters?: any;
-    enableTypeahead: boolean;
-    notApplicable: boolean;
-    notAvailable: boolean;
-    excelValidation?: any;
-    customValidationRules?: any;
-    apiEnhancements?: any;
-    visibility: string;
-    owner?: number;
-    ownerUsername?: string;
-    labGroup?: number;
-    labGroupName?: string;
-    schema?: number;
-    schemaName?: string;
-    sourceSchema?: string;
-    isSystemTemplate: boolean;
-    isActive: boolean;
-    usageCount?: number;
-    tags?: string[];
-    category?: string;
-    lastUsedAt?: string;
-    canEdit?: boolean;
-    canDelete?: boolean;
+interface ColumnOverrideMappingEntry {
+    fileColIndex: number;
+    columnId: number | null;
 }
-interface MetadataColumnTemplateShare extends BaseTimestampedModel {
-    id: number;
-    template: number;
-    templateName?: string;
-    sharedWith: number;
-    sharedWithUsername?: string;
-    sharedBy: number;
-    sharedByUsername?: string;
-    canEdit: boolean;
+interface ColumnOverrideImportOptions {
+    updateValue: boolean;
+    updateModifiers: boolean;
+    normalizeOntology?: boolean;
 }
-interface MetadataColumnTemplateCreateRequest {
-    name: string;
-    description?: string;
+interface ColumnOverrideSuggestResult {
+    fileHeaders: {
+        fileColIndex: number;
+        header: string;
+    }[];
+    tableColumns: {
+        columnId: number;
+        columnName: string;
+        columnPosition: number;
+    }[];
+    suggestedMapping: ColumnOverrideMappingEntry[];
+    fileRowCount: number;
+    tableSampleCount: number;
+}
+interface ColumnOverrideMatchedColumn {
+    columnId: number;
     columnName: string;
-    columnType: string;
-    defaultValue?: string;
-    defaultPosition?: number;
-    ontologyType?: string;
-    customOntologyFilters?: any;
-    enableTypeahead?: boolean;
-    notApplicable?: boolean;
-    notAvailable?: boolean;
-    excelValidation?: any;
-    customValidationRules?: any;
-    apiEnhancements?: any;
-    visibility?: string;
-    labGroup?: number;
-    tags?: string[];
-    category?: string;
+    fileHeader: string;
+    fileColIndex: number;
+    currentValue: string | null;
+    newValue: string | null;
+    currentModifiers: {
+        samples: string;
+        value: string;
+    }[];
+    newModifiers: {
+        samples: string;
+        value: string;
+    }[];
+    rowsChanged: number;
 }
-interface MetadataColumnTemplateUpdateRequest {
-    name?: string;
-    description?: string;
-    columnName?: string;
-    columnType?: string;
-    defaultValue?: string;
-    defaultPosition?: number;
-    ontologyType?: string;
-    customOntologyFilters?: any;
-    enableTypeahead?: boolean;
-    notApplicable?: boolean;
-    notAvailable?: boolean;
-    excelValidation?: any;
-    customValidationRules?: any;
-    apiEnhancements?: any;
-    visibility?: string;
-    isActive?: boolean;
-    tags?: string[];
-    category?: string;
+interface ColumnOverridePreviewResult {
+    columnsMatched: ColumnOverrideMatchedColumn[];
+    columnsToAdd: {
+        fileHeader: string;
+        fileColIndex: number;
+        columnType: string;
+        newValue: string | null;
+        newModifiers: {
+            samples: string;
+            value: string;
+        }[];
+        warning: string;
+    }[];
+    warnings: string[];
+    sampleCountMismatch: boolean;
+    fileRowCount: number;
 }
-interface MetadataColumnTemplateShareCreateRequest {
-    template: number;
-    sharedWith: number;
-    canEdit?: boolean;
+interface ColumnOverrideCommitResult {
+    message: string;
+    columnsUpdated: number;
+    columnsAdded: number;
+    warnings: string[];
+    updatedColumns: {
+        id: number;
+        name: string;
+    }[];
 }
 
 interface MetadataTableTemplate extends BaseTimestampedModel {
@@ -441,6 +552,19 @@ interface MetadataTableTemplateQueryResponse {
     previous?: string;
     results: MetadataTableTemplate[];
 }
+interface MetadataTableTemplateSyncRequest {
+    add_new?: boolean;
+    update_existing?: boolean;
+    remove_orphans?: boolean;
+}
+interface MetadataTableTemplateSyncResponse {
+    message: string;
+    added: number;
+    updated: number;
+    removed: number;
+    errors: string[];
+    schemas: string[];
+}
 
 interface FavouriteMetadataOption extends BaseTimestampedModel {
     id: number;
@@ -547,6 +671,21 @@ interface CellOntology {
     synonyms?: any;
     crossReferences?: any;
 }
+interface BTOTerm {
+    identifier: string;
+    name: string;
+    synonyms?: any;
+    definition?: string;
+    xrefs?: any;
+}
+interface DiseaseOntologyTerm {
+    identifier: string;
+    name: string;
+    synonyms?: any;
+    definition?: string;
+    xrefs?: any;
+}
+type SchemaLayer = 'technology' | 'sample' | 'experiment' | '';
 interface Schema {
     id: number;
     name: string;
@@ -554,6 +693,12 @@ interface Schema {
     description?: string;
     category?: string;
     version?: string;
+    extends?: string;
+    usableAlone?: boolean;
+    layer?: SchemaLayer;
+    requires?: any[];
+    excludes?: any;
+    tags?: string[];
     url?: string;
     isActive: boolean;
     isBuiltin: boolean;
@@ -561,6 +706,23 @@ interface Schema {
     creator?: number;
     creatorUsername?: string;
     columnsCount?: number;
+    usageCount?: number;
+}
+interface SchemaColumn {
+    id: number;
+    columnName: string;
+    columnType: string;
+    name: string;
+    ontologyType: string | null;
+    ontologyOptions: string[];
+    customOntologyFilters: Record<string, unknown>;
+    enableTypeahead: boolean;
+    inputType: string;
+    possibleDefaultValues: string[];
+    units: string[];
+    notApplicable: boolean;
+    notAvailable: boolean;
+    validators: unknown[];
 }
 interface OntologySuggestion {
     id: string;
@@ -692,6 +854,12 @@ interface ChunkedUploadRequest {
     metadataTableId?: number;
     createPools?: boolean;
     replaceExisting?: boolean;
+    overrideSampleCount?: boolean;
+    validateOnly?: boolean;
+    schemaNames?: string[];
+    skipOntology?: boolean;
+    useOlsCacheOnly?: boolean;
+    applySchemaTemplates?: boolean;
 }
 interface ChunkedUploadResponse {
     id: string;
@@ -706,6 +874,12 @@ interface ChunkedUploadCompletionRequest {
     metadataTableId?: number;
     createPools?: boolean;
     replaceExisting?: boolean;
+    overrideSampleCount?: boolean;
+    validateOnly?: boolean;
+    schemaNames?: string[];
+    skipOntology?: boolean;
+    useOlsCacheOnly?: boolean;
+    applySchemaTemplates?: boolean;
 }
 interface ChunkedUploadCompletionResponse {
     message?: string;
@@ -715,6 +889,31 @@ interface ChunkedUploadCompletionResponse {
     taskId?: string;
 }
 
+interface ExcelLaunchRequest {
+    tableId: number;
+    tableName?: string;
+}
+interface ExcelLaunchCode {
+    code: string;
+    tableId: number;
+    tableName?: string;
+    expiresIn: number;
+}
+interface ExcelLaunchClaimRequest {
+    code: string;
+}
+interface ExcelLaunchClaimResponse {
+    accessToken: string;
+    refreshToken: string;
+    tableId: number;
+    tableName?: string;
+    user: {
+        id: number;
+        username: string;
+        email: string;
+    };
+}
+
 interface MetadataTableQueryParams {
     search?: string;
     ownerId?: number;
@@ -725,6 +924,10 @@ interface MetadataTableQueryParams {
     limit?: number;
     offset?: number;
     ordering?: string;
+    columnName?: string;
+    columnValue?: string;
+    columnType?: string;
+    columnMatch?: 'contains' | 'exact';
 }
 declare class MetadataTableService extends BaseApiService {
     /**
@@ -804,6 +1007,18 @@ declare class MetadataTableService extends BaseApiService {
      * Search metadata tables
      */
     searchMetadataTables(query: string): Observable<MetadataTableQueryResponse>;
+    /**
+     * Find tables that contain a column matching the given name and/or value
+     */
+    findByColumnContent(params: {
+        columnName?: string;
+        columnValue?: string;
+        columnType?: string;
+        columnMatch?: 'contains' | 'exact';
+        showShared?: boolean;
+        limit?: number;
+        offset?: number;
+    }): Observable<MetadataTableQueryResponse>;
     /**
      * Get metadata tables by owner
      */
@@ -895,6 +1110,9 @@ declare class MetadataTableService extends BaseApiService {
         staffOnly: boolean;
     }>;
     advancedAutofill(id: number, request: AdvancedAutofillRequest): Observable<AdvancedAutofillResponse>;
+    suggestColumnMapping(tableId: number, file: File, algorithm: 'name' | 'position' | 'none'): Observable<ColumnOverrideSuggestResult>;
+    previewColumnOverride(tableId: number, file: File, mapping: ColumnOverrideMappingEntry[], options: ColumnOverrideImportOptions): Observable<ColumnOverridePreviewResult>;
+    commitColumnOverride(tableId: number, file: File, mapping: ColumnOverrideMappingEntry[], options: ColumnOverrideImportOptions): Observable<ColumnOverrideCommitResult>;
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<MetadataTableService, never>;
     static ɵprov: _angular_core.ɵɵInjectableDeclaration<MetadataTableService>;
 }
@@ -1236,6 +1454,9 @@ declare class MetadataTableTemplateService extends BaseApiService {
         schemaIds: number[];
         name: string;
         description?: string;
+        labGroup?: number | null;
+        visibility?: string;
+        isDefault?: boolean;
     }): Observable<{
         message: string;
         template: MetadataTableTemplate;
@@ -1248,6 +1469,7 @@ declare class MetadataTableTemplateService extends BaseApiService {
         name: string;
         description?: string;
         sampleCount: number;
+        labGroup?: number;
     }): Observable<MetadataTable>;
     /**
      * Create a new metadata table directly from schema definitions
@@ -1287,6 +1509,11 @@ declare class MetadataTableTemplateService extends BaseApiService {
         }>;
         staffOnly: boolean;
     }>;
+    /**
+     * Sync template columns from linked schemas.
+     * Updates existing columns with latest ontology settings and optionally adds new columns.
+     */
+    syncFromSchemas(id: number, request?: MetadataTableTemplateSyncRequest): Observable<MetadataTableTemplateSyncResponse>;
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<MetadataTableTemplateService, never>;
     static ɵprov: _angular_core.ɵɵInjectableDeclaration<MetadataTableTemplateService>;
 }
@@ -1341,12 +1568,20 @@ interface MetadataColumnTemplateQueryParams {
     labGroupId?: number;
     visibility?: string;
     isActive?: boolean;
+    isSystemTemplate?: boolean;
     schemaId?: number;
     sourceSchema?: string;
+    inputType?: string;
     limit?: number;
     offset?: number;
     ordering?: string;
 }
+interface GroupedColumnTemplateQueryParams {
+    search?: string;
+    isSystemTemplate?: boolean;
+    limit?: number;
+    offset?: number;
+}
 declare class MetadataColumnTemplateService extends BaseApiService {
     /**
      * Get all metadata column templates with optional filtering
@@ -1425,6 +1660,14 @@ declare class MetadataColumnTemplateService extends BaseApiService {
         customFilters: any;
         hasMore: boolean;
     }>;
+    /**
+     * Get column templates grouped by (column_name, column_type)
+     */
+    getGroupedColumnTemplates(params?: GroupedColumnTemplateQueryParams): Observable<PaginatedResponse<GroupedColumnTemplate>>;
+    /**
+     * Get all templates for a specific column name and type
+     */
+    getTemplatesByColumnNameAndType(columnName: string, columnType: string): Observable<MetadataColumnTemplate[]>;
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<MetadataColumnTemplateService, never>;
     static ɵprov: _angular_core.ɵɵInjectableDeclaration<MetadataColumnTemplateService>;
 }
@@ -1490,14 +1733,6 @@ declare class MetadataManagementService extends BaseApiService {
     static ɵprov: _angular_core.ɵɵInjectableDeclaration<MetadataManagementService>;
 }
 
-declare class Websocket extends WebSocketService {
-    constructor(authService: AuthService);
-    getMetadataTableUpdates(): Observable<WebSocketMessage>;
-    getLabGroupUpdates(): Observable<WebSocketMessage>;
-    static ɵfac: _angular_core.ɵɵFactoryDeclaration<Websocket, never>;
-    static ɵprov: _angular_core.ɵɵInjectableDeclaration<Websocket>;
-}
-
 declare enum NotificationType {
     SYSTEM = "system",
     METADATA_TABLE = "metadata_table",
@@ -1511,7 +1746,7 @@ declare class NotificationService extends NotificationService$1 {
     private websocketService;
     private isConnected;
     readonly isWebSocketConnected: _angular_core.Signal<boolean>;
-    constructor(websocketService: Websocket, toastService: ToastService);
+    constructor();
     private initializeWebSocket;
     private setupNotificationHandlers;
     private handleWebSocketMessage;
@@ -1595,6 +1830,10 @@ declare class SchemaService extends BaseApiService {
      * Get list of available schemas for creating templates
      */
     getAvailableSchemas(): Observable<Schema[]>;
+    /**
+     * Get columns for a schema by its integer ID
+     */
+    getSchemaColumns(id: number): Observable<SchemaColumn[]>;
     /**
      * Sync builtin schemas from sdrf-pipelines package (admin only)
      */
@@ -1679,6 +1918,98 @@ declare class SDRFDefaultsService extends BaseApiService {
     static ɵprov: _angular_core.ɵɵInjectableDeclaration<SDRFDefaultsService>;
 }
 
+interface ColumnConfig {
+    columnName: string;
+    inputType: ColumnInputType;
+    validators: ColumnValidator[];
+    units: string[];
+    possibleValues: (string | number)[];
+    description: string;
+    schemaName?: string;
+}
+declare class OfficialColumnCacheService {
+    private columnTemplateService;
+    private columnsByName;
+    private columnsBySchema;
+    private columnsByKey;
+    private isLoaded;
+    private isLoading;
+    readonly loaded: _angular_core.Signal<boolean>;
+    readonly loading: _angular_core.Signal<boolean>;
+    readonly columnCount: _angular_core.Signal<number>;
+    readonly uniqueColumnNames: _angular_core.Signal<number>;
+    constructor(columnTemplateService: MetadataColumnTemplateService);
+    /**
+     * Initialize the cache by loading all official (system) column templates.
+     * Call this on app initialization or when first needed.
+     */
+    initialize(): Observable<boolean>;
+    private fetchAllSystemTemplates;
+    /**
+     * Get all column templates with a given name (may exist in multiple schemas).
+     */
+    getColumns(columnName: string): MetadataColumnTemplate[];
+    /**
+     * Get column template by name and schema.
+     * Use this when you need the exact configuration for a specific schema.
+     */
+    getColumn(columnName: string, schemaName?: string): MetadataColumnTemplate | undefined;
+    /**
+     * Get column configuration with a simplified interface.
+     * If schema is specified, returns that specific config.
+     * Otherwise returns the first found (typically base schema).
+     */
+    getColumnConfig(columnName: string, schemaName?: string): ColumnConfig | undefined;
+    /**
+     * Get merged configuration from all schemas for a column.
+     * Combines possible values and units from all schema variants.
+     */
+    getMergedColumnConfig(columnName: string): ColumnConfig | undefined;
+    /**
+     * Get all columns for a specific schema.
+     */
+    getColumnsBySchema(schemaName: string): MetadataColumnTemplate[];
+    /**
+     * Get all available schema names.
+     */
+    getSchemaNames(): string[];
+    /**
+     * Search for columns by partial name match.
+     * Returns all variants across all schemas.
+     */
+    searchColumns(query: string): MetadataColumnTemplate[];
+    /**
+     * Get columns filtered by input type.
+     */
+    getColumnsByInputType(inputType: ColumnInputType): MetadataColumnTemplate[];
+    /**
+     * Check if a column exists in official schemas.
+     */
+    hasColumn(columnName: string): boolean;
+    /**
+     * Get all schemas that define a specific column.
+     */
+    getSchemasForColumn(columnName: string): string[];
+    /**
+     * Get possible values for a column, merged from all schemas.
+     */
+    getPossibleValues(columnName: string): (string | number)[];
+    /**
+     * Get units for a number_with_unit column, merged from all schemas.
+     */
+    getUnits(columnName: string): string[];
+    /**
+     * Clear the cache (useful for testing or forced refresh).
+     */
+    clear(): void;
+    /**
+     * Force refresh the cache.
+     */
+    refresh(): Observable<boolean>;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<OfficialColumnCacheService, never>;
+    static ɵprov: _angular_core.ɵɵInjectableDeclaration<OfficialColumnCacheService>;
+}
+
 declare class AsyncTaskService extends BaseApiService {
     /**
      * Get all async tasks for the current user with optional filtering
@@ -1715,6 +2046,24 @@ declare class AsyncExportService extends BaseApiService {
     static ɵprov: _angular_core.ɵɵInjectableDeclaration<AsyncExportService>;
 }
 
+declare class AsyncImportService extends BaseApiService {
+    private chunkedUploadService;
+    constructor();
+    sdrfFile(request: MetadataImportRequest): Observable<AsyncTaskCreateResponse>;
+    excelFile(request: MetadataImportRequest): Observable<AsyncTaskCreateResponse>;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<AsyncImportService, never>;
+    static ɵprov: _angular_core.ɵɵInjectableDeclaration<AsyncImportService>;
+}
+
+declare class AsyncValidationService extends BaseApiService {
+    private chunkedUploadService;
+    getAvailableSchemas(): Observable<ValidationSchema[]>;
+    metadataTable(request: MetadataValidationRequest): Observable<AsyncTaskCreateResponse>;
+    sdrfFile(request: SdrfFileValidationRequest): Observable<AsyncTaskCreateResponse>;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<AsyncValidationService, never>;
+    static ɵprov: _angular_core.ɵɵInjectableDeclaration<AsyncValidationService>;
+}
+
 declare class ChunkedUploadService extends BaseApiService {
     private siteConfigService;
     /**
@@ -1740,40 +2089,30 @@ declare class ChunkedUploadService extends BaseApiService {
     /**
      * Helper method to upload a file in chunks with progress tracking
      */
-    uploadFileInChunks(file: File, chunkSize?: number, // 1MB chunks by default
-    options?: {
+    uploadFileInChunks(file: File, chunkSize?: number, options?: {
         metadataTableId?: number;
         createPools?: boolean;
         replaceExisting?: boolean;
+        overrideSampleCount?: boolean;
         uploadSessionId?: string;
+        validateOnly?: boolean;
+        schemaNames?: string[];
+        skipOntology?: boolean;
+        useOlsCacheOnly?: boolean;
+        applySchemaTemplates?: boolean;
         onProgress?: (progress: number) => void;
     }): Observable<ChunkedUploadCompletionResponse>;
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<ChunkedUploadService, never>;
     static ɵprov: _angular_core.ɵɵInjectableDeclaration<ChunkedUploadService>;
 }
 
-declare class AsyncImportService extends BaseApiService {
-    private chunkedUploadService;
-    constructor(chunkedUploadService: ChunkedUploadService);
-    sdrfFile(request: MetadataImportRequest): Observable<AsyncTaskCreateResponse>;
-    excelFile(request: MetadataImportRequest): Observable<AsyncTaskCreateResponse>;
-    static ɵfac: _angular_core.ɵɵFactoryDeclaration<AsyncImportService, never>;
-    static ɵprov: _angular_core.ɵɵInjectableDeclaration<AsyncImportService>;
-}
-
-declare class AsyncValidationService extends BaseApiService {
-    getAvailableSchemas(): Observable<ValidationSchema[]>;
-    metadataTable(request: MetadataValidationRequest): Observable<AsyncTaskCreateResponse>;
-    static ɵfac: _angular_core.ɵɵFactoryDeclaration<AsyncValidationService, never>;
-    static ɵprov: _angular_core.ɵɵInjectableDeclaration<AsyncValidationService>;
-}
-
 interface ChunkedFileImportRequest {
     file: File;
     metadataTableId: number;
     replaceExisting?: boolean;
     validateOntologies?: boolean;
     createPools?: boolean;
+    applySchemaTemplates?: boolean;
 }
 interface ChunkedImportProgress {
     uploadProgress: number;
@@ -1782,7 +2121,7 @@ interface ChunkedImportProgress {
 }
 declare class ChunkedImportService extends BaseApiService {
     private chunkedUploadService;
-    constructor(chunkedUploadService: ChunkedUploadService);
+    constructor();
     /**
      * Import SDRF file using chunked upload for better performance with large files
      */
@@ -1912,9 +2251,23 @@ declare class SdrfSyntaxService {
     static ɵprov: _angular_core.ɵɵInjectableDeclaration<SdrfSyntaxService>;
 }
 
-interface ElectronAPI {
-    platform: string;
-    isElectron: boolean;
+declare class Websocket extends WebSocketService {
+    constructor();
+    getMetadataTableUpdates(): Observable<WebSocketMessage>;
+    getLabGroupUpdates(): Observable<WebSocketMessage>;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<Websocket, never>;
+    static ɵprov: _angular_core.ɵɵInjectableDeclaration<Websocket>;
+}
+
+/**
+ * @deprecated Use DesktopService instead. ElectronService is kept for backwards compatibility.
+ */
+declare class ElectronService {
+    private desktop;
+    get isElectron(): boolean;
+    get isWails(): boolean;
+    get isDesktop(): boolean;
+    get platform(): string;
     getAppVersion(): Promise<string>;
     getElectronVersion(): Promise<string>;
     minimize(): void;
@@ -1927,16 +2280,30 @@ interface ElectronAPI {
     downloadFile(url: string, filename?: string): Promise<string>;
     getBackendPort(): Promise<number>;
     isBackendReady(): Promise<boolean>;
-    onBackendStatusChange(callback: (status: any) => void): () => void;
-    onWindowStateChange(callback: (state: 'maximized' | 'unmaximized') => void): () => void;
+    onBackendStatusChange(): Observable<any>;
+    onWindowStateChange(): Observable<'maximized' | 'unmaximized'>;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<ElectronService, never>;
+    static ɵprov: _angular_core.ɵɵInjectableDeclaration<ElectronService>;
 }
-declare class ElectronService {
-    private electronAPI;
+
+declare class DesktopService {
+    private ngZone;
+    private readonly _runtime;
+    private backendStatusSubject;
+    private windowStateSubject;
+    private wailsRuntime;
     constructor();
+    private loadWailsRuntime;
+    private hasElectron;
+    private hasWails;
+    get runtime(): DesktopRuntime;
+    get isDesktop(): boolean;
     get isElectron(): boolean;
+    get isWails(): boolean;
     get platform(): string;
+    private setupWailsListeners;
     getAppVersion(): Promise<string>;
-    getElectronVersion(): Promise<string>;
+    getRuntimeVersion(): Promise<string>;
     minimize(): void;
     maximize(): void;
     close(): void;
@@ -1949,8 +2316,16 @@ declare class ElectronService {
     isBackendReady(): Promise<boolean>;
     onBackendStatusChange(): Observable<any>;
     onWindowStateChange(): Observable<'maximized' | 'unmaximized'>;
-    static ɵfac: _angular_core.ɵɵFactoryDeclaration<ElectronService, never>;
-    static ɵprov: _angular_core.ɵɵInjectableDeclaration<ElectronService>;
+    logToFile(message: string): Promise<void>;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<DesktopService, never>;
+    static ɵprov: _angular_core.ɵɵInjectableDeclaration<DesktopService>;
+}
+
+declare class ExcelLaunchService extends BaseApiService {
+    createLaunchCode(request: ExcelLaunchRequest): Observable<ExcelLaunchCode>;
+    claimLaunchCode(code: string): Observable<ExcelLaunchClaimResponse>;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<ExcelLaunchService, never>;
+    static ɵprov: _angular_core.ɵɵInjectableDeclaration<ExcelLaunchService>;
 }
 
 declare class SdrfAgeInput implements OnInit {
@@ -1960,6 +2335,7 @@ declare class SdrfAgeInput implements OnInit {
     private sdrfSyntax;
     ageForm: FormGroup;
     isRange: boolean;
+    constructor();
     ngOnInit(): void;
     private parseAndSetValue;
     private updateValue;
@@ -1988,6 +2364,7 @@ declare class SdrfModificationInput implements OnInit {
     showSpecifications: _angular_core.WritableSignal<boolean>;
     showHiddenSpecifications: _angular_core.WritableSignal<boolean>;
     hiddenSpecificationCount: _angular_core.WritableSignal<number>;
+    constructor();
     ngOnInit(): void;
     private parseAndSetValue;
     private getStringValue;
@@ -2017,6 +2394,7 @@ declare class SdrfSpikedCompoundInput implements OnInit {
     private sdrfSyntax;
     spikedForm: FormGroup;
     compoundTypes: string[];
+    constructor();
     ngOnInit(): void;
     private parseAndSetValue;
     private getStringValue;
@@ -2038,6 +2416,7 @@ declare class SdrfCleavageInput implements OnInit {
     private metadataColumnService;
     private metadataColumnTemplateService;
     cleavageForm: FormGroup;
+    constructor();
     ngOnInit(): void;
     private parseAndSetValue;
     private getStringValue;
@@ -2050,6 +2429,45 @@ declare class SdrfCleavageInput implements OnInit {
     static ɵcmp: _angular_core.ɵɵComponentDeclaration<SdrfCleavageInput, "ccv-sdrf-cleavage-input", never, { "value": { "alias": "value"; "required": false; }; "templateId": { "alias": "templateId"; "required": false; }; "columnId": { "alias": "columnId"; "required": false; }; }, { "valueChange": "valueChange"; }, never, never, true, never>;
 }
 
+declare class SdrfNumberWithUnitInput implements OnInit, OnChanges {
+    private fb;
+    value: string;
+    units: string[];
+    placeholder: string;
+    description: string;
+    examples: (string | number)[];
+    valueChange: EventEmitter<string>;
+    form: FormGroup;
+    constructor(fb: FormBuilder);
+    ngOnInit(): void;
+    ngOnChanges(changes: SimpleChanges): void;
+    private parseAndSetValue;
+    private updateValue;
+    selectExample(example: string | number): void;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<SdrfNumberWithUnitInput, never>;
+    static ɵcmp: _angular_core.ɵɵComponentDeclaration<SdrfNumberWithUnitInput, "ccv-sdrf-number-with-unit-input", never, { "value": { "alias": "value"; "required": false; }; "units": { "alias": "units"; "required": false; }; "placeholder": { "alias": "placeholder"; "required": false; }; "description": { "alias": "description"; "required": false; }; "examples": { "alias": "examples"; "required": false; }; }, { "valueChange": "valueChange"; }, never, never, true, never>;
+}
+
+declare class SdrfSelectInput implements OnInit, OnChanges {
+    value: string;
+    options: string[];
+    placeholder: string;
+    description: string;
+    allowCustom: boolean;
+    valueChange: EventEmitter<string>;
+    selectedValue: _angular_core.WritableSignal<string>;
+    isCustomMode: _angular_core.WritableSignal<boolean>;
+    customValue: _angular_core.WritableSignal<string>;
+    ngOnInit(): void;
+    ngOnChanges(changes: SimpleChanges): void;
+    private initializeValue;
+    onSelectionChange(value: string): void;
+    onCustomValueChange(value: string): void;
+    toggleCustomMode(): void;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<SdrfSelectInput, never>;
+    static ɵcmp: _angular_core.ɵɵComponentDeclaration<SdrfSelectInput, "ccv-sdrf-select-input", never, { "value": { "alias": "value"; "required": false; }; "options": { "alias": "options"; "required": false; }; "placeholder": { "alias": "placeholder"; "required": false; }; "description": { "alias": "description"; "required": false; }; "allowCustom": { "alias": "allowCustom"; "required": false; }; }, { "valueChange": "valueChange"; }, never, never, true, never>;
+}
+
 interface MetadataValueEditConfig {
     columnId?: number;
     columnName: string;
@@ -2071,6 +2489,10 @@ interface MetadataValueEditConfig {
     maxSampleCount?: number;
     allowNotApplicable?: boolean;
     allowNotAvailable?: boolean;
+    inputType?: ColumnInputType;
+    validators?: ColumnValidator[];
+    units?: string[];
+    possibleDefaultValues?: (string | number)[];
 }
 declare class MetadataValueEditModal implements OnInit {
     private fb;
@@ -2102,10 +2524,17 @@ declare class MetadataValueEditModal implements OnInit {
     specialSyntaxType: _angular_core.WritableSignal<SyntaxType | null>;
     showSpecialInput: _angular_core.WritableSignal<boolean>;
     specialInputValue: _angular_core.WritableSignal<string>;
+    validatorInputType: _angular_core.WritableSignal<ColumnInputType | null>;
+    validatorUnits: _angular_core.WritableSignal<string[]>;
+    validatorOptions: _angular_core.WritableSignal<string[]>;
+    validatorDescription: _angular_core.WritableSignal<string>;
+    validatorExamples: _angular_core.WritableSignal<(string | number)[]>;
     selectedSampleIndices: _angular_core.WritableSignal<Set<number>>;
     showSamplePanel: _angular_core.WritableSignal<boolean>;
     constructor(fb: FormBuilder, activeModal: NgbActiveModal, authService: AuthService, favouriteMetadataOptionService: FavouriteMetadataOptionService, metadataColumnService: MetadataColumnService, metadataColumnTemplateService: MetadataColumnTemplateService, labGroupService: LabGroupService, ontologySearchService: OntologySearchService);
     ngOnInit(): void;
+    private initializeValidatorInputType;
+    onValidatorInputChange(value: string): void;
     onCancel(): void;
     onClose(): void;
     get title(): string;
@@ -2270,9 +2699,9 @@ declare class AsyncTaskUIService implements OnDestroy {
     private toastService;
     private asyncTaskMonitor;
     private modalService;
-    private electronService;
-    tasks$: Observable<AsyncTaskStatus[]>;
-    activeTasks$: Observable<AsyncTaskStatus[]>;
+    private desktopService;
+    tasks: _angular_core.Signal<AsyncTaskStatus[]>;
+    activeTasks: _angular_core.Signal<AsyncTaskStatus[]>;
     metadataTableRefresh$: Observable<number>;
     taskCompleted$: Observable<AsyncTaskStatus>;
     exportTaskCompleted$: Observable<AsyncTaskStatus>;
@@ -2370,6 +2799,11 @@ declare class MetadataTableTemplates implements OnInit {
      * Perform the actual template column reordering with async task monitoring
      */
     private performTemplateColumnReorder;
+    /**
+     * Sync template columns from linked schemas.
+     * Updates columns with latest ontology settings and adds new columns from schemas.
+     */
+    syncTemplateFromSchemas(template: MetadataTableTemplate): void;
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<MetadataTableTemplates, never>;
     static ɵcmp: _angular_core.ɵɵComponentDeclaration<MetadataTableTemplates, "ccv-metadata-table-templates", never, {}, {}, never, never, true, never>;
 }
@@ -2434,7 +2868,9 @@ declare class ColumnEditModal implements OnInit {
     private activeModal;
     private modalService;
     private metadataColumnTemplateService;
+    private schemaService;
     private sdrfSyntaxService;
+    private officialColumnCache;
     column: MetadataColumn | null;
     templateId: number | null;
     isEdit: boolean;
@@ -2455,13 +2891,13 @@ declare class ColumnEditModal implements OnInit {
     totalTemplates: number;
     totalTemplatePages: number;
     Math: Math;
-    officialSdrfColumns: SdrfColumnConfig[];
-    showOfficialColumns: boolean;
-    selectedOfficialColumn: SdrfColumnConfig | null;
-    availableOfficialColumns: SdrfColumnConfig[];
+    showSystemTemplatesOnly: boolean;
+    selectedSchemaFilter: string;
+    availableSchemas: Schema[];
+    validationError: _angular_core.WritableSignal<string | null>;
     showTemplateSwap: boolean;
     showCreateCustomTemplate: boolean;
-    constructor(fb: FormBuilder, activeModal: NgbActiveModal, modalService: NgbModal, metadataColumnTemplateService: MetadataColumnTemplateService, sdrfSyntaxService: SdrfSyntaxService);
+    constructor(fb: FormBuilder, activeModal: NgbActiveModal, modalService: NgbModal, metadataColumnTemplateService: MetadataColumnTemplateService, schemaService: SchemaService, sdrfSyntaxService: SdrfSyntaxService, officialColumnCache: OfficialColumnCacheService);
     ngOnInit(): void;
     private populateForm;
     private getOntologyTypeIndex;
@@ -2476,17 +2912,15 @@ declare class ColumnEditModal implements OnInit {
     openValueEditModal(): void;
     setDefaultValue(value: string): void;
     private loadColumnTemplates;
+    private loadAvailableSchemas;
+    toggleSystemTemplatesFilter(systemOnly: boolean): void;
+    onSchemaFilterChange(schema: string): void;
     onTemplateFilterChange(): void;
     clearTemplateFilter(): void;
     onTemplatePageChange(page: number): void;
     onTemplateSelectionChange(): void;
     clearTemplate(): void;
     getOntologyTypeLabel(ontologyType: string): string;
-    toggleOfficialColumns(): void;
-    selectOfficialColumn(column: SdrfColumnConfig): void;
-    private filterOfficialColumns;
-    private getOntologyConfigForColumn;
-    private isColumnMandatory;
     showTemplateSwapOptions(): void;
     swapToTemplate(template: MetadataColumnTemplate): void;
     showCreateCustomTemplateOption(): void;
@@ -2495,6 +2929,7 @@ declare class ColumnEditModal implements OnInit {
     toggleAdvancedMode(): void;
     onOntologyTypeChange(event: Event): void;
     private getCorrectedColumnType;
+    private getOntologyConfigForColumn;
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<ColumnEditModal, never>;
     static ɵcmp: _angular_core.ɵɵComponentDeclaration<ColumnEditModal, "ccv-column-edit-modal", never, { "column": { "alias": "column"; "required": false; }; "templateId": { "alias": "templateId"; "required": false; }; "isEdit": { "alias": "isEdit"; "required": false; }; }, { "columnSaved": "columnSaved"; }, never, never, true, never>;
 }
@@ -2503,26 +2938,48 @@ interface TemplateSchemaSelectionResult {
     name: string;
     description: string;
     schemaIds: number[];
-    labGroupId?: number;
+    labGroup?: number;
     visibility: ResourceVisibility;
     isDefault: boolean;
 }
-declare class TemplateSchemaSelectionModal {
+interface SchemasByLayer {
+    technology: Schema[];
+    sample: Schema[];
+    experiment: Schema[];
+    other: Schema[];
+}
+declare class TemplateSchemaSelectionModal implements OnInit {
     private fb;
     activeModal: NgbActiveModal;
-    availableSchemas: any[];
+    private _availableSchemas;
+    set availableSchemas(value: Schema[]);
+    get availableSchemas(): Schema[];
     labGroups: any[];
     templateCreated: EventEmitter<TemplateSchemaSelectionResult>;
     templateForm: FormGroup;
     selectedSchemas: _angular_core.WritableSignal<Set<number>>;
+    schemasByLayer: _angular_core.WritableSignal<SchemasByLayer>;
+    layerInfo: Record<string, {
+        label: string;
+        icon: string;
+        description: string;
+        color: string;
+    }>;
     selectedSchemasCount: _angular_core.Signal<number>;
     constructor(fb: FormBuilder, activeModal: NgbActiveModal);
+    ngOnInit(): void;
+    private groupSchemasByLayer;
+    getLayerKeys(): string[];
+    hasLayerSchemas(layer: string): boolean;
+    getLayerSchemas(layer: string): Schema[];
     toggleSchema(schemaId: number): void;
     onSchemaCheckChange(event: Event, schemaId: number): void;
     isSchemaSelected(schemaId: number): boolean;
     getSelectedSchemas(): number[];
     removeSchema(schemaId: number): void;
+    getSchemaById(schemaId: number): Schema | undefined;
     getSchemaDisplayName(schemaId: number): string;
+    getSchemaLayer(schemaId: number): string;
     private updateDescription;
     canCreateTemplate(): boolean;
     onCreateTemplate(): void;
@@ -2536,14 +2993,14 @@ interface TableCreationData {
     templateId: number;
     sampleCount?: number;
     description?: string;
-    labGroupId?: number;
+    labGroup?: number;
 }
 declare class TableCreationModalComponent implements OnInit {
     private fb;
     activeModal: NgbActiveModal;
     template: MetadataTableTemplate;
     labGroups: LabGroup[];
-    selectedLabGroupId?: number;
+    selectedLabGroup?: number;
     tableCreated: EventEmitter<TableCreationData>;
     tableForm: FormGroup;
     isCreating: boolean;
@@ -2557,7 +3014,7 @@ declare class TableCreationModalComponent implements OnInit {
     getFieldError(fieldName: string): string | null;
     private getFieldLabel;
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<TableCreationModalComponent, never>;
-    static ɵcmp: _angular_core.ɵɵComponentDeclaration<TableCreationModalComponent, "ccv-table-creation-modal", never, { "template": { "alias": "template"; "required": false; }; "labGroups": { "alias": "labGroups"; "required": false; }; "selectedLabGroupId": { "alias": "selectedLabGroupId"; "required": false; }; }, { "tableCreated": "tableCreated"; }, never, never, true, never>;
+    static ɵcmp: _angular_core.ɵɵComponentDeclaration<TableCreationModalComponent, "ccv-table-creation-modal", never, { "template": { "alias": "template"; "required": false; }; "labGroups": { "alias": "labGroups"; "required": false; }; "selectedLabGroup": { "alias": "selectedLabGroup"; "required": false; }; }, { "tableCreated": "tableCreated"; }, never, never, true, never>;
 }
 
 interface SchemaSelectionResult {
@@ -2610,6 +3067,7 @@ declare class ColumnTemplates implements OnInit {
     columnFilter: _angular_core.WritableSignal<string>;
     sortField: _angular_core.WritableSignal<string>;
     sortDirection: _angular_core.WritableSignal<"asc" | "desc">;
+    viewMode: _angular_core.WritableSignal<"flat" | "grouped">;
     templatesData: _angular_core.WritableSignal<{
         count: number;
         results: MetadataColumnTemplate[];
@@ -2619,11 +3077,23 @@ declare class ColumnTemplates implements OnInit {
     selectedSchema: _angular_core.WritableSignal<Schema | null>;
     schemaSearchText: string;
     schemaTypeFilter: _angular_core.WritableSignal<"user" | "all" | "builtin">;
+    groupedTemplatesData: _angular_core.WritableSignal<{
+        count: number;
+        results: GroupedColumnTemplate[];
+    }>;
+    expandedGroups: _angular_core.WritableSignal<Set<string>>;
+    groupTemplatesCache: _angular_core.WritableSignal<Map<string, MetadataColumnTemplate[]>>;
+    loadingGroups: _angular_core.WritableSignal<Set<string>>;
+    isLoadingGrouped: _angular_core.WritableSignal<boolean>;
+    groupedCurrentPage: _angular_core.WritableSignal<number>;
+    groupedPageSize: _angular_core.WritableSignal<number>;
     hasTemplates: _angular_core.Signal<boolean>;
     hasLabGroups: _angular_core.Signal<boolean>;
     hasSchemas: _angular_core.Signal<boolean>;
     showTemplatesPagination: _angular_core.Signal<boolean>;
     showLabGroupsPagination: _angular_core.Signal<boolean>;
+    hasGroupedTemplates: _angular_core.Signal<boolean>;
+    showGroupedPagination: _angular_core.Signal<boolean>;
     filteredTemplates: _angular_core.Signal<MetadataColumnTemplate[]>;
     constructor(fb: FormBuilder, metadataColumnTemplateService: MetadataColumnTemplateService, labGroupService: LabGroupService, schemaService: SchemaService, modalService: NgbModal);
     ngOnInit(): void;
@@ -2658,6 +3128,17 @@ declare class ColumnTemplates implements OnInit {
     deleteTemplate(template: MetadataColumnTemplate): void;
     duplicateTemplate(template: MetadataColumnTemplate): void;
     private refreshTemplates;
+    setViewMode(mode: 'flat' | 'grouped'): void;
+    private loadGroupedTemplates;
+    onGroupedPageChange(page: number): void;
+    getGroupKey(group: GroupedColumnTemplate): string;
+    isGroupExpanded(group: GroupedColumnTemplate): boolean;
+    isGroupLoading(group: GroupedColumnTemplate): boolean;
+    toggleGroup(group: GroupedColumnTemplate): void;
+    private loadGroupTemplates;
+    getGroupTemplates(group: GroupedColumnTemplate): MetadataColumnTemplate[];
+    collapseAllGroups(): void;
+    expandAllGroups(): void;
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<ColumnTemplates, never>;
     static ɵcmp: _angular_core.ɵɵComponentDeclaration<ColumnTemplates, "ccv-column-templates", never, {}, {}, never, never, true, never>;
 }
@@ -2705,13 +3186,6 @@ declare class ColumnTemplateEditModal implements OnInit {
 }
 
 declare class FavoriteManagement implements OnInit {
-    private fb;
-    private favouriteMetadataOptionService;
-    private metadataColumnTemplateService;
-    private labGroupService;
-    private toastService;
-    private modalService;
-    private authService;
     Math: Math;
     isLoading: _angular_core.WritableSignal<boolean>;
     favorites: _angular_core.WritableSignal<FavouriteMetadataOption[]>;
@@ -2731,10 +3205,17 @@ declare class FavoriteManagement implements OnInit {
     editingFavorite: _angular_core.WritableSignal<FavouriteMetadataOption | null>;
     showEditModal: _angular_core.WritableSignal<boolean>;
     private sdrfSyntaxService;
+    private fb;
+    private favouriteMetadataOptionService;
+    private metadataColumnTemplateService;
+    private labGroupService;
+    private toastService;
+    private modalService;
+    private authService;
     specialSyntaxType: _angular_core.WritableSignal<SyntaxType | null>;
     showSpecialInput: _angular_core.WritableSignal<boolean>;
     specialInputValue: _angular_core.WritableSignal<string>;
-    currentUser: _angular_core.WritableSignal<User | null>;
+    currentUser: _angular_core.Signal<User | null>;
     isAdmin: _angular_core.Signal<boolean>;
     currentUserId: _angular_core.Signal<number | null>;
     userLabGroups: _angular_core.WritableSignal<LabGroup[]>;
@@ -2754,7 +3235,7 @@ declare class FavoriteManagement implements OnInit {
         value: string;
         label: string;
     }[];
-    constructor(fb: FormBuilder, favouriteMetadataOptionService: FavouriteMetadataOptionService, metadataColumnTemplateService: MetadataColumnTemplateService, labGroupService: LabGroupService, toastService: ToastService, modalService: NgbModal, authService: AuthService);
+    constructor();
     ngOnInit(): void;
     loadFavorites(): void;
     canEditFavorite(favorite: FavouriteMetadataOption): boolean;
@@ -2857,6 +3338,7 @@ declare class MetadataTableDetails implements OnInit, OnDestroy {
     private toastService;
     private asyncTaskService;
     private modalService;
+    private officialColumnCache;
     private destroy$;
     fileInput: ElementRef<HTMLInputElement>;
     excelInput: ElementRef<HTMLInputElement>;
@@ -2869,6 +3351,8 @@ declare class MetadataTableDetails implements OnInit, OnDestroy {
     getSortIcon(field: string): string;
     isSorted(field: string): boolean;
     isLoading: _angular_core.WritableSignal<boolean>;
+    overrideSampleCount: _angular_core.WritableSignal<boolean>;
+    applySchemaTemplates: _angular_core.WritableSignal<boolean>;
     table: _angular_core.WritableSignal<MetadataTable | null>;
     tableId: _angular_core.WritableSignal<number | null>;
     viewMode: _angular_core.WritableSignal<"list" | "table">;
@@ -2886,7 +3370,7 @@ declare class MetadataTableDetails implements OnInit, OnDestroy {
     poolTableRows: _angular_core.Signal<any[]>;
     paginatedRows: _angular_core.Signal<any[]>;
     totalPages: _angular_core.Signal<number>;
-    constructor(route: ActivatedRoute, router: Router, metadataTableService: MetadataTableService, asyncExportService: AsyncExportService, chunkedUploadService: ChunkedUploadService, samplePoolService: SamplePoolService, metadataColumnService: MetadataColumnService, toastService: ToastService, asyncTaskService: AsyncTaskUIService, modalService: NgbModal);
+    constructor(route: ActivatedRoute, router: Router, metadataTableService: MetadataTableService, asyncExportService: AsyncExportService, chunkedUploadService: ChunkedUploadService, samplePoolService: SamplePoolService, metadataColumnService: MetadataColumnService, toastService: ToastService, asyncTaskService: AsyncTaskUIService, modalService: NgbModal, officialColumnCache: OfficialColumnCacheService);
     ngOnInit(): void;
     ngOnDestroy(): void;
     private setupAsyncTaskRefreshListener;
@@ -2931,6 +3415,7 @@ declare class MetadataTableDetails implements OnInit, OnDestroy {
     viewColumnDetails(column: MetadataColumn): void;
     editColumnSettings(column: MetadataColumn): void;
     openColumnHistory(column: MetadataColumn): void;
+    openColumnOverrideImportModal(): void;
     private updateColumnSettings;
     editPoolColumnValue(pool: SamplePool, column: any): void;
     editSampleColumnValue(column: MetadataColumn, sampleIndex: number): void;
@@ -3103,18 +3588,17 @@ interface ColumnHistoryModalConfig {
     columnName: string;
 }
 declare class MetadataColumnHistoryModal implements OnInit {
-    activeModal: NgbActiveModal;
-    private columnService;
     config: ColumnHistoryModalConfig;
     closed: EventEmitter<void>;
-    history: MetadataColumnHistoryRecord[];
-    loading: boolean;
-    error: string | null;
-    totalCount: number;
-    limit: number;
-    offset: number;
-    hasMore: boolean;
-    constructor(activeModal: NgbActiveModal, columnService: MetadataColumnService);
+    readonly history: _angular_core.WritableSignal<MetadataColumnHistoryRecord[]>;
+    readonly loading: _angular_core.WritableSignal<boolean>;
+    readonly error: _angular_core.WritableSignal<string | null>;
+    readonly totalCount: _angular_core.WritableSignal<number>;
+    readonly hasMore: _angular_core.WritableSignal<boolean>;
+    private limit;
+    private offset;
+    readonly activeModal: NgbActiveModal;
+    private columnService;
     ngOnInit(): void;
     loadHistory(): void;
     loadMore(): void;
@@ -3126,10 +3610,88 @@ declare class MetadataColumnHistoryModal implements OnInit {
     static ɵcmp: _angular_core.ɵɵComponentDeclaration<MetadataColumnHistoryModal, "ccv-metadata-column-history-modal", never, { "config": { "alias": "config"; "required": false; }; }, { "closed": "closed"; }, never, never, true, never>;
 }
 
+declare class OpenInExcel {
+    private launchService;
+    readonly tableId: _angular_core.InputSignal<number>;
+    readonly tableName: _angular_core.InputSignal<string>;
+    readonly buttonClass: _angular_core.InputSignal<string>;
+    readonly showIcon: _angular_core.InputSignal<boolean>;
+    readonly buttonText: _angular_core.InputSignal<string>;
+    readonly launched: _angular_core.OutputEmitterRef<ExcelLaunchCode>;
+    readonly error: _angular_core.OutputEmitterRef<string>;
+    readonly isLoading: _angular_core.WritableSignal<boolean>;
+    readonly launchCode: _angular_core.WritableSignal<ExcelLaunchCode | null>;
+    readonly showModal: _angular_core.WritableSignal<boolean>;
+    readonly copySuccess: _angular_core.WritableSignal<boolean>;
+    createLaunchCode(): void;
+    copyCode(): void;
+    closeModal(): void;
+    getExpiryTime(): string;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<OpenInExcel, never>;
+    static ɵcmp: _angular_core.ɵɵComponentDeclaration<OpenInExcel, "ccv-open-in-excel", never, { "tableId": { "alias": "tableId"; "required": true; "isSignal": true; }; "tableName": { "alias": "tableName"; "required": false; "isSignal": true; }; "buttonClass": { "alias": "buttonClass"; "required": false; "isSignal": true; }; "showIcon": { "alias": "showIcon"; "required": false; "isSignal": true; }; "buttonText": { "alias": "buttonText"; "required": false; "isSignal": true; }; }, { "launched": "launched"; "error": "error"; }, never, never, true, never>;
+}
+
+interface ColumnOverrideImportModalConfig {
+    tableId: number;
+    tableName: string;
+    sampleCount: number;
+}
+type Step = 'upload' | 'map' | 'preview' | 'confirming' | 'done';
+declare class ColumnOverrideImportModal {
+    config: ColumnOverrideImportModalConfig;
+    private activeModal;
+    private tableService;
+    private fb;
+    readonly step: _angular_core.WritableSignal<Step>;
+    readonly selectedFile: _angular_core.WritableSignal<File | null>;
+    readonly isLoading: _angular_core.WritableSignal<boolean>;
+    readonly error: _angular_core.WritableSignal<string | null>;
+    readonly suggestResult: _angular_core.WritableSignal<ColumnOverrideSuggestResult | null>;
+    readonly userMapping: _angular_core.WritableSignal<ColumnOverrideMappingEntry[]>;
+    readonly previewResult: _angular_core.WritableSignal<ColumnOverridePreviewResult | null>;
+    readonly commitResult: _angular_core.WritableSignal<ColumnOverrideCommitResult | null>;
+    readonly optionsForm: FormGroup;
+    readonly mappedColumnIds: _angular_core.Signal<Set<number>>;
+    readonly newColumnCount: _angular_core.Signal<number>;
+    onFileChange(event: Event): void;
+    generateMapping(): void;
+    updateMappingEntry(fileColIndex: number, value: string): void;
+    removeMappingEntry(fileColIndex: number): void;
+    restoreMappingEntry(fileColIndex: number): void;
+    isIgnored(fileColIndex: number): boolean;
+    getColumnIdForFileCol(fileColIndex: number): string;
+    reapplyAlgorithm(): void;
+    preview(): void;
+    confirm(): void;
+    backToUpload(): void;
+    backToMap(): void;
+    close(): void;
+    dismiss(): void;
+    private buildOptions;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<ColumnOverrideImportModal, never>;
+    static ɵcmp: _angular_core.ɵɵComponentDeclaration<ColumnOverrideImportModal, "ccv-column-override-import-modal", never, { "config": { "alias": "config"; "required": false; }; }, {}, never, never, true, never>;
+}
+
 declare class CupcakeVanilla {
     static ɵfac: _angular_core.ɵɵFactoryDeclaration<CupcakeVanilla, never>;
     static ɵcmp: _angular_core.ɵɵComponentDeclaration<CupcakeVanilla, "ccv-cupcake-vanilla", never, {}, {}, never, never, true, never>;
 }
 
-export { AsyncExportService, AsyncImportService, AsyncTaskService, AsyncTaskUIService, AsyncValidationService, COLUMN_TYPE_CONFIGS, ChunkedImportService, ChunkedUploadService, ColumnEditModal, ColumnTemplateEditModal, ColumnTemplates, ColumnType, CupcakeVanilla, ElectronService, ExcelExportModalComponent, FavoriteManagement, FavouriteMetadataOptionService, MSTermType, MetadataColumnAutofillModal, MetadataColumnHistoryModal, MetadataColumnService, MetadataColumnTemplateService, MetadataColumnTemplateShareService, MetadataManagementService, MetadataTableDetails, MetadataTableEditModal, MetadataTableService, MetadataTableTemplateEditModal, MetadataTableTemplateService, MetadataTableTemplates, MetadataValidationModal, MetadataValueEditModal, NotificationService, NotificationType, OFFICIAL_SDRF_COLUMNS, ONTOLOGY_TYPE_CONFIGS, OntologySearchService, OntologyType, OntologyTypeLabels, OntologyUtils, SDRFDefaultsService, SamplePoolCreateModal, SamplePoolDetailsModal, SamplePoolEditModal, SamplePoolService, SchemaSelectionModal, SchemaService, SdrfAgeInput, SdrfCleavageInput, SdrfColumnCategory, SdrfModificationInput, SdrfSpikedCompoundInput, SdrfSyntaxService, SearchReplaceModal, TableCreationModalComponent, TemplatePermissionLabels, TemplatePermissionLevel, TemplateSchemaSelectionModal, ValidationResultsModal, Websocket, getRequiredSdrfColumns, getSdrfColumnByName, getSdrfColumnsByCategory, isSdrfColumnRequired, isUnimodFullData };
-export type { AdvancedAutofillRequest, AdvancedAutofillResponse, AgeFormat, ApiResponse, BaseTimestampedModel, CellOntology, ChEBICompound, ChunkedFileImportRequest, ChunkedImportProgress, ChunkedUploadCompletionRequest, ChunkedUploadCompletionResponse, ChunkedUploadRequest, ChunkedUploadResponse, ChunkedUploadStatus, CleavageAgentDetails, ColumnHistoryModalConfig, ColumnTypeConfig, ElectronAPI, ExcelExportOptions, FavouriteMetadataOption, FavouriteMetadataOptionCreateRequest, FavouriteMetadataOptionQueryParams, FavouriteMetadataOptionUpdateRequest, HumanDisease, MSUniqueVocabularies, MetadataColumn, MetadataColumnAutofillConfig, MetadataColumnCreateRequest, MetadataColumnHistoryChange, MetadataColumnHistoryRecord, MetadataColumnHistoryResponse, MetadataColumnHistorySnapshot, MetadataColumnModifier, MetadataColumnQueryParams, MetadataColumnTemplate, MetadataColumnTemplateCreateRequest, MetadataColumnTemplateQueryParams, MetadataColumnTemplateShare, MetadataColumnTemplateShareCreateRequest, MetadataColumnTemplateShareQueryParams, MetadataColumnTemplateUpdateRequest, MetadataColumnUpdateRequest, MetadataQueryParams, MetadataTable, MetadataTableCreateRequest, MetadataTableQueryParams, MetadataTableQueryResponse, MetadataTableTemplate, MetadataTableTemplateCreateRequest, MetadataTableTemplateQueryParams, MetadataTableTemplateQueryResponse, MetadataTableTemplateUpdateRequest, MetadataTableUpdateRequest, MetadataValueEditConfig, ModificationParameters, MondoDisease, NCBITaxonomy, OntologyCustomFilter, OntologySuggestParams, OntologySuggestResponse, OntologySuggestion, OntologyTypeConfig, PSIMSOntology, PaginatedResponse, PooledSample, SampleCountConfirmationError, SampleCountValidationRequest, SampleCountValidationResponse, SampleCountValidationResult, SamplePool, SamplePoolCreateRequest, SamplePoolQueryParams, SamplePoolUpdateRequest, Schema, SchemaQueryParams, SchemaSelectionResult, SdrfColumnConfig, SearchReplaceConfig, Species, SpikedCompound, SubcellularLocation, SyntaxType, SyntheticPeptide, TableCreationData, TemplateSchemaSelectionResult, Tissue, UberonAnatomy, Unimod, UnimodFullData, UnimodSpecification, ValidationResult, ValidationResults, VariationSpec, VariationSpecList, VariationSpecPattern, VariationSpecRange };
+declare class DualScrollDirective implements AfterViewInit, OnDestroy {
+    private el;
+    private renderer;
+    private topBar;
+    private topBarInner;
+    private resizeObserver;
+    private readonly onHostScroll;
+    private readonly onTopScroll;
+    constructor(el: ElementRef<HTMLElement>, renderer: Renderer2);
+    ngAfterViewInit(): void;
+    private syncWidth;
+    ngOnDestroy(): void;
+    static ɵfac: _angular_core.ɵɵFactoryDeclaration<DualScrollDirective, never>;
+    static ɵdir: _angular_core.ɵɵDirectiveDeclaration<DualScrollDirective, "[appDualScroll]", never, {}, {}, never, never, true, never>;
+}
+
+export { AsyncExportService, AsyncImportService, AsyncTaskService, AsyncTaskUIService, AsyncValidationService, COLUMN_TYPE_CONFIGS, ChunkedImportService, ChunkedUploadService, ColumnEditModal, ColumnOverrideImportModal, ColumnTemplateEditModal, ColumnTemplates, ColumnType, CupcakeVanilla, DesktopService, DualScrollDirective, ElectronService, ExcelExportModalComponent, ExcelLaunchService, FavoriteManagement, FavouriteMetadataOptionService, MSTermType, MetadataColumnAutofillModal, MetadataColumnHistoryModal, MetadataColumnService, MetadataColumnTemplateService, MetadataColumnTemplateShareService, MetadataManagementService, MetadataTableDetails, MetadataTableEditModal, MetadataTableService, MetadataTableTemplateEditModal, MetadataTableTemplateService, MetadataTableTemplates, MetadataValidationModal, MetadataValueEditModal, NotificationService, NotificationType, OFFICIAL_SDRF_COLUMNS, ONTOLOGY_TYPE_CONFIGS, OfficialColumnCacheService, OntologySearchService, OntologyType, OntologyTypeLabels, OntologyUtils, OpenInExcel, SDRFDefaultsService, SamplePoolCreateModal, SamplePoolDetailsModal, SamplePoolEditModal, SamplePoolService, SchemaSelectionModal, SchemaService, SdrfAgeInput, SdrfCleavageInput, SdrfColumnCategory, SdrfModificationInput, SdrfNumberWithUnitInput, SdrfSelectInput, SdrfSpikedCompoundInput, SdrfSyntaxService, SearchReplaceModal, TableCreationModalComponent, TemplatePermissionLabels, TemplatePermissionLevel, TemplateSchemaSelectionModal, ValidationResultsModal, Websocket, createSyntheticColumnFromTemplate, getRequiredSdrfColumns, getSdrfColumnByName, getSdrfColumnsByCategory, isSdrfColumnRequired, isUnimodFullData };
+export type { AdvancedAutofillRequest, AdvancedAutofillResponse, AgeFormat, ApiError, ApiResponse, BTOTerm, BaseTimestampedModel, CellOntology, ChEBICompound, ChunkedFileImportRequest, ChunkedImportProgress, ChunkedUploadCompletionRequest, ChunkedUploadCompletionResponse, ChunkedUploadRequest, ChunkedUploadResponse, ChunkedUploadStatus, CleavageAgentDetails, ColumnConfig, ColumnHistoryModalConfig, ColumnInputType, ColumnOverrideCommitResult, ColumnOverrideImportModalConfig, ColumnOverrideImportOptions, ColumnOverrideMappingEntry, ColumnOverrideMatchedColumn, ColumnOverridePreviewResult, ColumnOverrideSuggestResult, ColumnTypeConfig, ColumnValidator, DiseaseOntologyTerm, ExcelExportOptions, ExcelLaunchClaimRequest, ExcelLaunchClaimResponse, ExcelLaunchCode, ExcelLaunchRequest, FavouriteMetadataOption, FavouriteMetadataOptionCreateRequest, FavouriteMetadataOptionQueryParams, FavouriteMetadataOptionUpdateRequest, GroupedColumnTemplate, GroupedColumnTemplateQueryParams, HumanDisease, MSUniqueVocabularies, MetadataColumn, MetadataColumnAutofillConfig, MetadataColumnCreateRequest, MetadataColumnHistoryChange, MetadataColumnHistoryRecord, MetadataColumnHistoryResponse, MetadataColumnHistorySnapshot, MetadataColumnModifier, MetadataColumnQueryParams, MetadataColumnTemplate, MetadataColumnTemplateCreateRequest, MetadataColumnTemplateQueryParams, MetadataColumnTemplateShare, MetadataColumnTemplateShareCreateRequest, MetadataColumnTemplateShareQueryParams, MetadataColumnTemplateUpdateRequest, MetadataColumnUpdateRequest, MetadataQueryParams, MetadataTable, MetadataTableCreateRequest, MetadataTableQueryParams, MetadataTableQueryResponse, MetadataTableTemplate, MetadataTableTemplateCreateRequest, MetadataTableTemplateQueryParams, MetadataTableTemplateQueryResponse, MetadataTableTemplateSyncRequest, MetadataTableTemplateSyncResponse, MetadataTableTemplateUpdateRequest, MetadataTableUpdateRequest, MetadataValueEditConfig, ModificationParameters, MondoDisease, NCBITaxonomy, OntologyCustomFilter, OntologySuggestParams, OntologySuggestResponse, OntologySuggestion, OntologyTypeConfig, PSIMSOntology, PaginatedResponse, PooledSample, SampleCountConfirmationError, SampleCountValidationRequest, SampleCountValidationResponse, SampleCountValidationResult, SamplePool, SamplePoolCreateRequest, SamplePoolQueryParams, SamplePoolUpdateRequest, Schema, SchemaColumn, SchemaLayer, SchemaQueryParams, SchemaSelectionResult, SchemasByLayer, SdrfColumnConfig, SearchReplaceConfig, Species, SpikedCompound, SubcellularLocation, SyntaxType, SyntheticPeptide, TableCreationData, TemplateSchemaSelectionResult, Tissue, UberonAnatomy, Unimod, UnimodFullData, UnimodSpecification, ValidationResult, ValidationResults, VariationSpec, VariationSpecList, VariationSpecPattern, VariationSpecRange };