@noatgnu/cupcake-vanilla 1.0.0

package/index.d.ts

@@ -0,0 +1,1491 @@
+import * as i0 from '@angular/core';
+import { Observable } from 'rxjs';
+import { BaseApiService } from '@cupcake/core';
+
+interface BaseTimestampedModel {
+    createdAt: string;
+    updatedAt: string;
+}
+interface PaginatedResponse<T> {
+    count: number;
+    next?: string;
+    previous?: string;
+    results: T[];
+}
+interface ApiResponse<T = any> {
+    data?: T;
+    error?: any;
+    status: number;
+    success: boolean;
+}
+interface MetadataQueryParams {
+    page?: number;
+    pageSize?: number;
+    search?: string;
+    ordering?: string;
+    owner?: number;
+    labGroup?: number;
+    isPublished?: boolean;
+    includeLocked?: boolean;
+}
+
+declare enum OntologyType {
+    SPECIES = "species",
+    TISSUE = "tissue",
+    HUMAN_DISEASE = "human_disease",
+    SUBCELLULAR_LOCATION = "subcellular_location",
+    UNIMOD = "unimod",
+    NCBI_TAXONOMY = "ncbi_taxonomy",
+    MONDO = "mondo",
+    UBERON = "uberon",
+    CHEBI = "chebi",
+    CELL_ONTOLOGY = "cell_ontology",
+    MS_UNIQUE_VOCABULARIES = "ms_unique_vocabularies",
+    PSI_MS = "psi_ms"
+}
+declare const OntologyTypeLabels: Record<OntologyType, string>;
+declare enum TemplatePermissionLevel {
+    READ = "read",
+    WRITE = "write",
+    ADMIN = "admin"
+}
+declare const TemplatePermissionLabels: Record<TemplatePermissionLevel, string>;
+
+interface MetadataTable extends BaseTimestampedModel {
+    id: number;
+    name: string;
+    description?: string;
+    sampleCount: number;
+    version: string;
+    owner?: number;
+    ownerUsername?: string;
+    labGroup?: number;
+    labGroupName?: string;
+    isLocked: boolean;
+    isPublished: boolean;
+    visibility: 'private' | 'group' | 'public';
+    contentType?: number;
+    objectId?: number;
+    columns?: any[];
+    samplePools?: any[];
+    columnCount?: number;
+    sampleRange?: string;
+    canEdit?: boolean;
+    sourceApp?: string;
+}
+interface MetadataTableCreateRequest {
+    name: string;
+    description?: string;
+    sampleCount: number;
+    version?: string;
+    labGroup?: number;
+    isPublished?: boolean;
+    sourceApp?: string;
+}
+interface MetadataTableUpdateRequest {
+    name?: string;
+    description?: string;
+    sampleCount?: number;
+    version?: string;
+    isLocked?: boolean;
+    isPublished?: boolean;
+}
+interface MetadataTableQueryResponse {
+    count: number;
+    next?: string;
+    previous?: string;
+    results: MetadataTable[];
+}
+
+interface MetadataColumnModifier {
+    samples: string;
+    value: string;
+}
+interface MetadataColumn extends BaseTimestampedModel {
+    id: number;
+    metadataTable: number;
+    metadataTableName?: string;
+    template?: number;
+    templateName?: string;
+    name: string;
+    type: string;
+    columnPosition: number;
+    value?: string;
+    notApplicable: boolean;
+    mandatory: boolean;
+    hidden: boolean;
+    autoGenerated: boolean;
+    readonly: boolean;
+    modifiers: MetadataColumnModifier[];
+    ontologyType?: OntologyType;
+    ontologyOptions?: any;
+    suggestedValues: any[];
+    enableTypeahead: boolean;
+    possibleDefaultValues: any[];
+    staffOnly: boolean;
+}
+interface MetadataColumnCreateRequest {
+    metadataTable: number;
+    template?: number;
+    name: string;
+    type: string;
+    columnPosition?: number;
+    value?: string;
+    notApplicable?: boolean;
+    mandatory?: boolean;
+    hidden?: boolean;
+    autoGenerated?: boolean;
+    readonly?: boolean;
+    modifiers?: MetadataColumnModifier[];
+    ontologyType?: OntologyType;
+    ontologyOptions?: any;
+    enableTypeahead?: boolean;
+    staffOnly?: boolean;
+}
+interface MetadataColumnUpdateRequest {
+    name?: string;
+    type?: string;
+    columnPosition?: number;
+    value?: string;
+    notApplicable?: boolean;
+    mandatory?: boolean;
+    hidden?: boolean;
+    autoGenerated?: boolean;
+    readonly?: boolean;
+    modifiers?: MetadataColumnModifier[];
+    ontologyType?: OntologyType;
+    ontologyOptions?: any;
+    enableTypeahead?: boolean;
+    staffOnly?: boolean;
+}
+
+interface MetadataColumnTemplate extends BaseTimestampedModel {
+    id: number;
+    name: string;
+    description?: string;
+    columnName: string;
+    columnType: string;
+    defaultValue?: string;
+    defaultPosition?: number;
+    ontologyType?: string;
+    customOntologyFilters?: any;
+    enableTypeahead: boolean;
+    excelValidation?: any;
+    customValidationRules?: any;
+    apiEnhancements?: any;
+    visibility: string;
+    owner?: number;
+    ownerUsername?: string;
+    labGroup?: number;
+    labGroupName?: string;
+    isSystemTemplate: boolean;
+    isActive: boolean;
+    usageCount?: number;
+    tags?: string[];
+    category?: string;
+    lastUsedAt?: string;
+    canEdit?: boolean;
+    canDelete?: 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;
+    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;
+    excelValidation?: any;
+    customValidationRules?: any;
+    apiEnhancements?: any;
+    visibility?: string;
+    isActive?: boolean;
+    tags?: string[];
+    category?: string;
+}
+interface MetadataColumnTemplateShareCreateRequest {
+    template: number;
+    sharedWith: number;
+    canEdit?: boolean;
+}
+
+interface SamplePool extends BaseTimestampedModel {
+    id: number;
+    poolName: string;
+    poolDescription?: string;
+    pooledOnlySamples: number[];
+    pooledAndIndependentSamples: number[];
+    isReference: boolean;
+    sdrfValue?: string;
+    metadataTable: number;
+    metadataTableName?: string;
+    totalSamples?: number;
+    allSampleIndices?: number[];
+    metadataColumns: MetadataColumn[];
+}
+interface SamplePoolCreateRequest {
+    poolName: string;
+    poolDescription?: string;
+    pooledOnlySamples?: number[];
+    pooledAndIndependentSamples?: number[];
+    isReference?: boolean;
+    sdrfValue?: string;
+    metadataTable: number;
+}
+interface SamplePoolUpdateRequest {
+    poolName?: string;
+    poolDescription?: string;
+    pooledOnlySamples?: number[];
+    pooledAndIndependentSamples?: number[];
+    isReference?: boolean;
+    sdrfValue?: string;
+}
+
+interface MetadataTableTemplate extends BaseTimestampedModel {
+    id: number;
+    name: string;
+    description?: string;
+    owner?: number;
+    ownerUsername?: string;
+    labGroup?: number;
+    userColumns?: any[];
+    userColumnIds?: number[];
+    fieldMaskMapping?: any;
+    visibility?: string;
+    isDefault: boolean;
+    columnCount?: number;
+}
+interface MetadataTableTemplateCreateRequest {
+    name: string;
+    description?: string;
+    labGroup?: number;
+    userColumnIds?: number[];
+    fieldMaskMapping?: any;
+    visibility?: string;
+    isDefault?: boolean;
+}
+interface MetadataTableTemplateUpdateRequest {
+    name?: string;
+    description?: string;
+    userColumnIds?: number[];
+    fieldMaskMapping?: any;
+    visibility?: string;
+    isDefault?: boolean;
+}
+interface MetadataTableTemplateQueryResponse {
+    count: number;
+    next?: string;
+    previous?: string;
+    results: MetadataTableTemplate[];
+}
+
+interface FavouriteMetadataOption extends BaseTimestampedModel {
+    id: number;
+    name: string;
+    type: string;
+    columnTemplate?: number;
+    value: string;
+    displayValue?: string;
+    user?: number;
+    userUsername?: string;
+    labGroup?: number;
+    labGroupName?: string;
+    isGlobal: boolean;
+}
+interface FavouriteMetadataOptionCreateRequest {
+    name: string;
+    type: string;
+    columnTemplate?: number;
+    value: string;
+    displayValue?: string;
+    user?: number;
+    labGroup?: number;
+    isGlobal?: boolean;
+}
+interface FavouriteMetadataOptionUpdateRequest {
+    name?: string;
+    type?: string;
+    columnTemplate?: number;
+    value?: string;
+    displayValue?: string;
+    isGlobal?: boolean;
+}
+
+interface Species {
+    code: string;
+    taxon: string;
+    officialName: string;
+    commonName?: string;
+    synonym?: string;
+}
+interface Tissue {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface HumanDisease {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface SubcellularLocation {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface MSUniqueVocabularies {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface Unimod {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface MondoDisease {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface UberonAnatomy {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface NCBITaxonomy {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface ChEBICompound {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface PSIMSOntology {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface CellOntology {
+    identifier: string;
+    accession: string;
+    synonyms?: any;
+    crossReferences?: any;
+}
+interface Schema {
+    id: number;
+    name: string;
+    description?: string;
+    category?: string;
+    version?: string;
+    url?: string;
+    isActive: boolean;
+    columnsCount?: number;
+}
+interface OntologySuggestion {
+    id: string;
+    value: string;
+    display_name: string;
+    description?: string;
+    ontology_type: string;
+    full_data?: any;
+}
+interface OntologySuggestionResponse {
+    count: number;
+    next?: string;
+    previous?: string;
+    results: OntologySuggestion[];
+}
+
+interface UnimodSpecification {
+    accession: string;
+    name: string;
+    definition: string;
+    additional_data: Array<{
+        id: string;
+        description: string;
+    }>;
+    general_properties: Record<string, string>;
+    specifications: Record<string, UnimodSpecification>;
+    delta_mono_mass: string;
+    delta_avge_mass: string;
+    delta_composition: string;
+    [key: string]: any;
+}
+interface UnimodFullData {
+    accession: string;
+    name: string;
+    definition: string;
+    additional_data: Array<{
+        id: string;
+        description: string;
+    }>;
+    general_properties: Record<string, string>;
+    specifications: Record<string, UnimodSpecification>;
+    delta_mono_mass: string;
+    delta_avge_mass: string;
+    delta_composition: string;
+    [key: string]: any;
+}
+declare function isUnimodFullData(suggestion: any): suggestion is {
+    full_data: UnimodFullData;
+};
+declare class OntologyUtils {
+    static getUnimodSpecifications(suggestion: any): (UnimodSpecification & {
+        specNumber: string;
+    })[];
+    static getActiveUnimodSpecifications(suggestion: any): (UnimodSpecification & {
+        specNumber: string;
+    })[];
+    static formatUnimodName(data: UnimodFullData): string;
+}
+
+type TaskStatus = 'QUEUED' | 'STARTED' | 'SUCCESS' | 'FAILURE' | 'CANCELLED';
+type TaskType = 'EXPORT_EXCEL' | 'EXPORT_SDRF' | 'IMPORT_SDRF' | 'IMPORT_EXCEL' | 'EXPORT_MULTIPLE_SDRF' | 'EXPORT_MULTIPLE_EXCEL' | 'VALIDATE_TABLE';
+interface AsyncTaskStatus {
+    id: string;
+    taskType: TaskType;
+    status: TaskStatus;
+    user: number;
+    userUsername?: string;
+    metadataTable?: number;
+    metadataTableName?: string;
+    taskTypeDisplay?: string;
+    statusDisplay?: string;
+    parameters?: any;
+    result?: any;
+    errorMessage?: string;
+    traceback?: string;
+    createdAt: string;
+    startedAt?: string;
+    completedAt?: string;
+    rqJobId?: string;
+    queueName?: string;
+    progressCurrent?: number;
+    progressTotal?: number;
+    progressDescription?: string;
+    duration?: number;
+    progressPercentage?: number;
+}
+interface TaskListItem {
+    id: string;
+    taskType: TaskType;
+    taskTypeDisplay: string;
+    status: TaskStatus;
+    statusDisplay: string;
+    user: number;
+    userUsername: string;
+    metadataTable: number | null;
+    metadataTableName: string | null;
+    progressPercentage: number;
+    progressDescription: string;
+    createdAt: string;
+    startedAt: string | null;
+    completedAt: string | null;
+    duration: number | null;
+    errorMessage: string | null;
+}
+interface TaskResult {
+    id: number;
+    task: string;
+    file?: string;
+    fileName?: string;
+    contentType?: string;
+    fileSize?: number;
+    expiresAt: string;
+    downloadCount?: number;
+    lastDownloadedAt?: string;
+    createdAt: string;
+}
+interface MetadataExportRequest {
+    metadataTableId: number;
+    includePools?: boolean;
+    metadataColumnIds?: number[];
+    sampleNumber?: number;
+    exportFormat?: string;
+    labGroupIds?: number[];
+}
+interface BulkExportRequest {
+    metadataTableIds: number[];
+    includePools?: boolean;
+    validateSdrf?: boolean;
+}
+interface BulkExcelExportRequest extends BulkExportRequest {
+    metadataColumnIds?: number[];
+    labGroupIds?: number[];
+}
+interface MetadataImportRequest {
+    metadataTableId: number;
+    file: File;
+    replaceExisting?: boolean;
+    validateOntologies?: boolean;
+}
+interface MetadataValidationRequest {
+    metadataTableId: number;
+    validateSdrfFormat?: boolean;
+    includePools?: boolean;
+}
+interface MetadataValidationConfig {
+    metadataTableId: number;
+    metadataTableName: string;
+}
+interface AsyncTaskCreateResponse {
+    taskId: string;
+    message: string;
+}
+interface DownloadUrlResponse {
+    downloadUrl: string;
+    filename: string;
+    contentType: string;
+    fileSize: number;
+    expiresAt: string;
+    expiresInHours: number;
+}
+interface AsyncTaskQueryParams {
+    taskType?: string;
+    status?: string;
+    metadataTable?: number;
+    search?: string;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare const TASK_TYPE_LABELS: Record<TaskType, string>;
+declare const TASK_STATUS_LABELS: Record<TaskStatus, string>;
+declare const TASK_STATUS_COLORS: Record<TaskStatus, string>;
+
+interface ChunkedUploadStatus {
+    id: string;
+    file?: File;
+    filename?: string;
+    offset: number;
+    createdAt: string;
+    status: 'INCOMPLETE' | 'COMPLETE';
+    completedAt?: string;
+    originalFilename?: string;
+    mimeType?: string;
+    fileSize?: number;
+    uploadSessionId?: string;
+    checksum?: string;
+}
+interface ChunkedUploadRequest {
+    file: File;
+    filename?: string;
+    uploadSessionId?: string;
+    metadataTableId?: number;
+    createPools?: boolean;
+    replaceExisting?: boolean;
+}
+interface ChunkedUploadResponse {
+    id: string;
+    filename: string;
+    offset: number;
+    expires: string;
+    url?: string;
+    checksum?: string;
+}
+interface ChunkedUploadCompletionRequest {
+    sha256: string;
+    metadataTableId?: number;
+    createPools?: boolean;
+    replaceExisting?: boolean;
+}
+interface ChunkedUploadCompletionResponse {
+    message: string;
+    filename?: string;
+    warning?: string;
+    error?: string;
+    createdColumns?: number;
+    createdPools?: number;
+    sampleRows?: number;
+    metadataColumns?: Array<{
+        id: number;
+        name: string;
+        type: string;
+        position: number;
+    }>;
+    samplePools?: Array<{
+        id: number;
+        name: string;
+        totalSamples: number;
+        isReference: boolean;
+    }>;
+}
+
+interface MetadataTableQueryParams {
+    search?: string;
+    ownerId?: number;
+    labGroupId?: number;
+    isPublished?: boolean;
+    isLocked?: boolean;
+    showShared?: boolean;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare class MetadataTableService extends BaseApiService {
+    /**
+     * Get all metadata tables with optional filtering
+     */
+    getMetadataTables(params?: MetadataTableQueryParams): Observable<MetadataTableQueryResponse>;
+    /**
+     * Get a single metadata table by ID
+     */
+    getMetadataTable(id: number): Observable<MetadataTable>;
+    /**
+     * Create a new metadata table
+     */
+    createMetadataTable(table: MetadataTableCreateRequest): Observable<MetadataTable>;
+    /**
+     * Update an existing metadata table
+     */
+    updateMetadataTable(id: number, table: MetadataTableUpdateRequest): Observable<MetadataTable>;
+    /**
+     * Partially update a metadata table
+     */
+    patchMetadataTable(id: number, table: Partial<MetadataTableUpdateRequest>): Observable<MetadataTable>;
+    /**
+     * Delete a metadata table
+     */
+    deleteMetadataTable(id: number): Observable<void>;
+    /**
+     * Add a column to the metadata table
+     */
+    addColumn(id: number, columnData: any, position?: number): Observable<{
+        message: string;
+        column: MetadataColumn;
+    }>;
+    /**
+     * Add a column with automatic reordering
+     */
+    addColumnWithAutoReorder(id: number, request: {
+        columnData: any;
+    }): Observable<{
+        message: string;
+        column: MetadataColumn;
+        reordered: boolean;
+        schemaIdsUsed: number[];
+    }>;
+    /**
+     * Remove a column from the metadata table
+     */
+    removeColumn(id: number, columnId: number): Observable<{
+        message: string;
+    }>;
+    /**
+     * Reorder a column in the metadata table
+     */
+    reorderColumn(id: number, columnId: number, newPosition: number): Observable<{
+        message: string;
+    }>;
+    /**
+     * Normalize column positions
+     */
+    normalizeColumnPositions(id: number): Observable<{
+        message: string;
+    }>;
+    /**
+     * Get all tables (admin only)
+     */
+    getAdminAllTables(): Observable<MetadataTable[]>;
+    /**
+     * Search metadata tables
+     */
+    searchMetadataTables(query: string): Observable<MetadataTableQueryResponse>;
+    /**
+     * Get metadata tables by owner
+     */
+    getMetadataTablesByOwner(ownerId: number): Observable<MetadataTableQueryResponse>;
+    /**
+     * Get shared metadata tables
+     */
+    getSharedMetadataTables(): Observable<MetadataTableQueryResponse>;
+    /**
+     * Combine columns column-wise
+     */
+    combineColumnwise(request: {
+        columnIds: number[];
+    }): Observable<{
+        message: string;
+        combinedColumn: any;
+    }>;
+    /**
+     * Combine columns row-wise
+     */
+    combineRowwise(request: {
+        columnIds: number[];
+    }): Observable<{
+        message: string;
+        combinedColumn: any;
+    }>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<MetadataTableService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<MetadataTableService>;
+}
+
+interface MetadataColumnQueryParams {
+    search?: string;
+    metadataTableId?: number;
+    type?: string;
+    name?: string;
+    hidden?: boolean;
+    mandatory?: boolean;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare class MetadataColumnService extends BaseApiService {
+    /**
+     * Get all metadata columns with optional filtering
+     */
+    getMetadataColumns(params?: MetadataColumnQueryParams): Observable<PaginatedResponse<MetadataColumn>>;
+    /**
+     * Get a single metadata column by ID
+     */
+    getMetadataColumn(id: number): Observable<MetadataColumn>;
+    /**
+     * Create a new metadata column
+     */
+    createMetadataColumn(column: MetadataColumnCreateRequest): Observable<MetadataColumn>;
+    /**
+     * Update an existing metadata column
+     */
+    updateMetadataColumn(id: number, column: MetadataColumnUpdateRequest): Observable<MetadataColumn>;
+    /**
+     * Partially update a metadata column
+     */
+    patchMetadataColumn(id: number, column: Partial<MetadataColumnUpdateRequest>): Observable<MetadataColumn>;
+    /**
+     * Delete a metadata column
+     */
+    deleteMetadataColumn(id: number): Observable<void>;
+    /**
+     * Bulk create metadata columns
+     */
+    bulkCreate(request: {
+        columns: MetadataColumnCreateRequest[];
+    }): Observable<MetadataColumn[]>;
+    /**
+     * Validate SDRF data
+     */
+    validateSdrfData(request: {
+        metadataIds: number[];
+        sampleNumber?: number;
+    }): Observable<{
+        valid: boolean;
+        errors: any[];
+        sampleCount: number;
+    }>;
+    /**
+     * Get ontology suggestions for a column
+     */
+    getOntologySuggestions(params: {
+        columnId: number;
+        search?: string;
+        limit?: number;
+        searchType?: 'icontains' | 'istartswith' | 'exact';
+    }): Observable<{
+        ontologyType: string;
+        suggestions: OntologySuggestion[];
+        searchTerm: string;
+        searchType: string;
+        limit: number;
+        count: number;
+        customFilters: any;
+        hasMore: boolean;
+    }>;
+    /**
+     * Validate value against column's ontology
+     */
+    validateValue(id: number, request: {
+        value: string;
+    }): Observable<{
+        valid: boolean;
+        value: string;
+        ontologyType: string;
+        suggestions?: any[];
+    }>;
+    /**
+     * Update column value with automatic modifier calculation
+     */
+    updateColumnValue(id: number, request: {
+        value: string;
+        sampleIndices?: number[];
+        valueType?: 'default' | 'sample_specific' | 'replace_all';
+    }): Observable<{
+        message: string;
+        column: MetadataColumn;
+        changes: any;
+        valueType: string;
+    }>;
+    /**
+     * Apply automatic ontology mapping to a column
+     */
+    applyOntologyMapping(id: number): Observable<{
+        applied: boolean;
+        ontologyType: string;
+        message: string;
+    }>;
+    /**
+     * Detect ontology type for given column name and type
+     */
+    detectOntologyType(params: {
+        name: string;
+        type: string;
+    }): Observable<{
+        columnName: string;
+        columnType: string;
+        detectedOntologyType: string;
+    }>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<MetadataColumnService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<MetadataColumnService>;
+}
+
+interface SamplePoolQueryParams {
+    search?: string;
+    metadataTable?: number;
+    isReference?: boolean;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare class SamplePoolService extends BaseApiService {
+    /**
+     * Get all sample pools with optional filtering
+     */
+    getSamplePools(params?: SamplePoolQueryParams): Observable<PaginatedResponse<SamplePool>>;
+    /**
+     * Get a single sample pool by ID
+     */
+    getSamplePool(id: number): Observable<SamplePool>;
+    /**
+     * Create a new sample pool
+     */
+    createSamplePool(pool: SamplePoolCreateRequest): Observable<SamplePool>;
+    /**
+     * Update an existing sample pool
+     */
+    updateSamplePool(id: number, pool: SamplePoolUpdateRequest): Observable<SamplePool>;
+    /**
+     * Partially update a sample pool
+     */
+    patchSamplePool(id: number, pool: Partial<SamplePoolUpdateRequest>): Observable<SamplePool>;
+    /**
+     * Delete a sample pool
+     */
+    deleteSamplePool(id: number): Observable<void>;
+    /**
+     * Get metadata columns associated with this pool
+     */
+    getMetadataColumns(id: number): Observable<MetadataColumn[]>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SamplePoolService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<SamplePoolService>;
+}
+
+interface MetadataTableTemplateQueryParams {
+    search?: string;
+    ownerId?: number;
+    labGroupId?: number;
+    visibility?: string;
+    isDefault?: boolean;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare class MetadataTableTemplateService extends BaseApiService {
+    /**
+     * Get all metadata table templates with optional filtering
+     */
+    getMetadataTableTemplates(params?: MetadataTableTemplateQueryParams): Observable<MetadataTableTemplateQueryResponse>;
+    /**
+     * Get a single metadata table template by ID
+     */
+    getMetadataTableTemplate(id: number): Observable<MetadataTableTemplate>;
+    /**
+     * Create a new metadata table template
+     */
+    createMetadataTableTemplate(template: MetadataTableTemplateCreateRequest): Observable<MetadataTableTemplate>;
+    /**
+     * Update an existing metadata table template
+     */
+    updateMetadataTableTemplate(id: number, template: MetadataTableTemplateUpdateRequest): Observable<MetadataTableTemplate>;
+    /**
+     * Partially update a metadata table template
+     */
+    patchMetadataTableTemplate(id: number, template: Partial<MetadataTableTemplateUpdateRequest>): Observable<MetadataTableTemplate>;
+    /**
+     * Delete a metadata table template
+     */
+    deleteMetadataTableTemplate(id: number): Observable<void>;
+    /**
+     * Add a column to the template
+     */
+    addColumn(id: number, request: {
+        column_data: any;
+        position?: number;
+    }): Observable<{
+        message: string;
+        column: MetadataColumn;
+    }>;
+    /**
+     * Remove a column from the template
+     */
+    removeColumn(id: number, request: {
+        column_id: number;
+    }): Observable<{
+        message: string;
+    }>;
+    /**
+     * Reorder a column within the template
+     */
+    reorderColumn(id: number, request: {
+        column_id: number;
+        new_position: number;
+    }): Observable<{
+        message: string;
+    }>;
+    /**
+     * Add a column with automatic reordering
+     */
+    addColumnWithAutoReorder(id: number, request: {
+        columnData: any;
+    }): Observable<{
+        message: string;
+        column: MetadataColumn;
+        reordered: boolean;
+        schemaIdsUsed: number[];
+    }>;
+    /**
+     * Duplicate a column within the template
+     */
+    duplicateColumn(id: number, request: {
+        column_id: number;
+    }): Observable<{
+        message: string;
+        duplicated_column: MetadataColumn;
+    }>;
+    /**
+     * Normalize column positions
+     */
+    normalizeColumnPositions(id: number): Observable<{
+        message: string;
+    }>;
+    /**
+     * Apply this template to a metadata table
+     */
+    applyToMetadataTable(id: number, request: {
+        metadata_table_id: number;
+    }): Observable<{
+        message: string;
+        applied_columns: MetadataColumn[];
+    }>;
+    /**
+     * Update field mask for template
+     */
+    updateFieldMask(id: number, request: {
+        field_mask: any;
+    }): Observable<{
+        message: string;
+        field_mask: any;
+    }>;
+    /**
+     * Get field mask for template
+     */
+    getFieldMask(id: number): Observable<{
+        field_mask: any;
+    }>;
+    /**
+     * Get columns with field masks
+     */
+    getColumnsWithFieldMasks(id: number): Observable<{
+        columns: any[];
+    }>;
+    /**
+     * Get available schemas for creating templates
+     */
+    getAvailableSchemas(): Observable<Schema[]>;
+    /**
+     * Create a new template from schema definitions
+     */
+    createFromSchema(request: {
+        schemaIds: number[];
+        name: string;
+        description?: string;
+    }): Observable<{
+        message: string;
+        template: MetadataTableTemplate;
+    }>;
+    /**
+     * Create a new metadata table from an existing template
+     */
+    createTableFromTemplate(request: {
+        templateId: number;
+        name: string;
+        description?: string;
+        sampleCount: number;
+    }): Observable<{
+        message: string;
+        table: MetadataTable;
+    }>;
+    /**
+     * Create a new metadata table directly from schema definitions
+     */
+    createTableFromSchemas(request: {
+        schemaIds: number[];
+        name: string;
+        description?: string;
+        sampleCount: number;
+    }): Observable<{
+        message: string;
+        table: MetadataTable;
+    }>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<MetadataTableTemplateService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<MetadataTableTemplateService>;
+}
+
+interface FavouriteMetadataOptionQueryParams {
+    search?: string;
+    type?: string;
+    userId?: number;
+    labGroupId?: number;
+    isGlobal?: boolean;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare class FavouriteMetadataOptionService extends BaseApiService {
+    /**
+     * Get all favourite metadata options with optional filtering
+     */
+    getFavouriteMetadataOptions(params?: FavouriteMetadataOptionQueryParams): Observable<PaginatedResponse<FavouriteMetadataOption>>;
+    /**
+     * Get a single favourite metadata option by ID
+     */
+    getFavouriteMetadataOption(id: number): Observable<FavouriteMetadataOption>;
+    /**
+     * Create a new favourite metadata option
+     */
+    createFavouriteMetadataOption(option: FavouriteMetadataOptionCreateRequest): Observable<FavouriteMetadataOption>;
+    /**
+     * Update an existing favourite metadata option
+     */
+    updateFavouriteMetadataOption(id: number, option: FavouriteMetadataOptionUpdateRequest): Observable<FavouriteMetadataOption>;
+    /**
+     * Partially update a favourite metadata option
+     */
+    patchFavouriteMetadataOption(id: number, option: Partial<FavouriteMetadataOptionUpdateRequest>): Observable<FavouriteMetadataOption>;
+    /**
+     * Delete a favourite metadata option
+     */
+    deleteFavouriteMetadataOption(id: number): Observable<void>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<FavouriteMetadataOptionService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<FavouriteMetadataOptionService>;
+}
+
+interface MetadataColumnTemplateQueryParams {
+    search?: string;
+    type?: string;
+    ontologyType?: string;
+    isRequired?: boolean;
+    isPublic?: boolean;
+    ownerId?: number;
+    labGroupId?: number;
+    visibility?: string;
+    isActive?: boolean;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare class MetadataColumnTemplateService extends BaseApiService {
+    /**
+     * Get all metadata column templates with optional filtering
+     */
+    getMetadataColumnTemplates(params?: MetadataColumnTemplateQueryParams): Observable<PaginatedResponse<MetadataColumnTemplate>>;
+    /**
+     * Get a single metadata column template by ID
+     */
+    getMetadataColumnTemplate(id: number): Observable<MetadataColumnTemplate>;
+    /**
+     * Create a new metadata column template
+     */
+    createMetadataColumnTemplate(template: MetadataColumnTemplateCreateRequest): Observable<MetadataColumnTemplate>;
+    /**
+     * Update an existing metadata column template
+     */
+    updateMetadataColumnTemplate(id: number, template: MetadataColumnTemplateUpdateRequest): Observable<MetadataColumnTemplate>;
+    /**
+     * Partially update a metadata column template
+     */
+    patchMetadataColumnTemplate(id: number, template: Partial<MetadataColumnTemplateUpdateRequest>): Observable<MetadataColumnTemplate>;
+    /**
+     * Delete a metadata column template
+     */
+    deleteMetadataColumnTemplate(id: number): Observable<void>;
+    /**
+     * Create a MetadataColumn from this template
+     */
+    createMetadataColumn(id: number, request: {
+        metadataTableId: number;
+        columnPosition?: number;
+    }): Observable<{
+        message: string;
+        column: MetadataColumn;
+    }>;
+    /**
+     * Share this template with another user
+     */
+    shareTemplate(id: number, request: {
+        userId: number;
+        canEdit?: boolean;
+    }): Observable<{
+        message: string;
+    }>;
+    /**
+     * Remove template sharing for a user
+     */
+    unshareTemplate(id: number, request: {
+        userId: number;
+    }): Observable<{
+        message: string;
+    }>;
+    /**
+     * Get templates created by the current user
+     */
+    getMyTemplates(): Observable<MetadataColumnTemplate[]>;
+    /**
+     * Get most popular public templates
+     */
+    getPopularTemplates(): Observable<MetadataColumnTemplate[]>;
+    /**
+     * Get ontology suggestions for this column template
+     */
+    getOntologySuggestions(params?: {
+        search?: string;
+        templateId?: number;
+        limit?: number;
+        searchType?: 'icontains' | 'istartswith' | 'exact';
+    }): Observable<{
+        ontologyType: string;
+        suggestions: OntologySuggestion[];
+        searchTerm: string;
+        searchType: string;
+        limit: number;
+        count: number;
+        customFilters: any;
+        hasMore: boolean;
+    }>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<MetadataColumnTemplateService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<MetadataColumnTemplateService>;
+}
+
+interface MetadataColumnTemplateShareQueryParams {
+    template?: number;
+    sharedWith?: number;
+    sharedBy?: number;
+    canEdit?: boolean;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare class MetadataColumnTemplateShareService extends BaseApiService {
+    /**
+     * Get all template shares with optional filtering
+     */
+    getMetadataColumnTemplateShares(params?: MetadataColumnTemplateShareQueryParams): Observable<PaginatedResponse<MetadataColumnTemplateShare>>;
+    /**
+     * Get a single template share by ID
+     */
+    getMetadataColumnTemplateShare(id: number): Observable<MetadataColumnTemplateShare>;
+    /**
+     * Create a new template share
+     */
+    createMetadataColumnTemplateShare(share: MetadataColumnTemplateShareCreateRequest): Observable<MetadataColumnTemplateShare>;
+    /**
+     * Update an existing template share
+     */
+    updateMetadataColumnTemplateShare(id: number, share: {
+        canEdit?: boolean;
+    }): Observable<MetadataColumnTemplateShare>;
+    /**
+     * Delete a template share
+     */
+    deleteMetadataColumnTemplateShare(id: number): Observable<void>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<MetadataColumnTemplateShareService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<MetadataColumnTemplateShareService>;
+}
+
+declare class MetadataManagementService extends BaseApiService {
+    /**
+     * Export metadata as Excel template (matching original CUPCAKE)
+     */
+    exportExcelTemplate(request: any): Observable<Blob>;
+    /**
+     * Import metadata from SDRF file with intelligent column matching and schema organization
+     */
+    importSdrfFile(file: File, additionalData?: any): Observable<any>;
+    /**
+     * Import metadata from Excel file (matching original CUPCAKE)
+     */
+    importExcelFile(file: File, additionalData?: any): Observable<any>;
+    /**
+     * Collect metadata from metadata table
+     */
+    collectMetadata(params: any): Observable<any>;
+    /**
+     * Export metadata as SDRF file (matching original CUPCAKE)
+     */
+    exportSdrfFile(request: any): Observable<Blob>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<MetadataManagementService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<MetadataManagementService>;
+}
+
+declare class OntologySearchService extends BaseApiService {
+    /**
+     * Get ontology suggestions across all sources for SDRF validation
+     */
+    suggest(params?: {
+        query?: string;
+        sources?: string[];
+    }): Observable<OntologySuggestion[]>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<OntologySearchService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<OntologySearchService>;
+}
+
+interface SchemaQueryParams {
+    search?: string;
+    category?: string;
+    isActive?: boolean;
+    limit?: number;
+    offset?: number;
+    ordering?: string;
+}
+declare class SchemaService extends BaseApiService {
+    /**
+     * Get all schemas with optional filtering
+     */
+    getSchemas(params?: SchemaQueryParams): Observable<PaginatedResponse<Schema>>;
+    /**
+     * Get a single schema by ID
+     */
+    getSchema(id: number): Observable<Schema>;
+    /**
+     * Get list of available schemas for creating templates
+     */
+    getAvailableSchemas(): Observable<Schema[]>;
+    /**
+     * Sync builtin schemas from sdrf-pipelines package (admin only)
+     */
+    syncBuiltin(): Observable<{
+        message: string;
+        synced_count: number;
+    }>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SchemaService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<SchemaService>;
+}
+
+declare class SDRFDefaultsService extends BaseApiService {
+    /**
+     * Get all available SDRF columns with their default values
+     */
+    getColumns(): Observable<any[]>;
+    /**
+     * Get default values for a specific column
+     */
+    getColumnValues(params: {
+        column: string;
+    }): Observable<any[]>;
+    /**
+     * Search for columns containing the query string
+     */
+    searchColumns(params: {
+        query: string;
+    }): Observable<any[]>;
+    /**
+     * Get options for structured fields (key-value pairs)
+     */
+    getStructuredOptions(params: {
+        field: string;
+    }): Observable<any[]>;
+    /**
+     * Get all label options (TMT, SILAC, label-free)
+     */
+    getLabels(): Observable<any[]>;
+    /**
+     * Get protein modification options (fixed and variable)
+     */
+    getModifications(): Observable<any[]>;
+    /**
+     * Get list of common instrument models
+     */
+    getInstruments(): Observable<any[]>;
+    /**
+     * Get cleavage agent options
+     */
+    getCleavageAgents(): Observable<any[]>;
+    /**
+     * Get all compound fields that require special handling
+     */
+    getCompoundFields(): Observable<any[]>;
+    /**
+     * Get schema for a specific compound field
+     */
+    getCompoundSchema(params: {
+        field: string;
+    }): Observable<any>;
+    /**
+     * Validate a compound field value against its schema
+     */
+    validateCompound(request: {
+        field: string;
+        value: any;
+    }): Observable<{
+        valid: boolean;
+        errors?: string[];
+    }>;
+    /**
+     * Get column name suggestions based on partial input
+     */
+    getSuggestions(params: {
+        query: string;
+    }): Observable<string[]>;
+    /**
+     * Get quick access to commonly used value categories
+     */
+    getQuickValues(): Observable<any>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SDRFDefaultsService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<SDRFDefaultsService>;
+}
+
+declare class AsyncTaskService extends BaseApiService {
+    /**
+     * Get all async tasks for the current user with optional filtering
+     */
+    getAsyncTasks(params?: AsyncTaskQueryParams): Observable<PaginatedResponse<AsyncTaskStatus>>;
+    /**
+     * Get a specific async task by ID
+     */
+    getAsyncTask(id: string): Observable<AsyncTaskStatus>;
+    /**
+     * Cancel a queued or running task
+     */
+    cancelTask(id: string): Observable<{
+        message: string;
+    }>;
+    /**
+     * Generate a signed download URL for task result file
+     */
+    getDownloadUrl(id: string): Observable<DownloadUrlResponse>;
+    /**
+     * Direct download endpoint (returns blob for file download)
+     */
+    downloadTaskFile(id: string, token: string): Observable<Blob>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<AsyncTaskService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<AsyncTaskService>;
+}
+
+declare class AsyncExportService extends BaseApiService {
+    excelTemplate(request: MetadataExportRequest): Observable<AsyncTaskCreateResponse>;
+    sdrfFile(request: MetadataExportRequest): Observable<AsyncTaskCreateResponse>;
+    multipleSdrfFiles(request: BulkExportRequest): Observable<AsyncTaskCreateResponse>;
+    multipleExcelTemplates(request: BulkExcelExportRequest): Observable<AsyncTaskCreateResponse>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<AsyncExportService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<AsyncExportService>;
+}
+
+declare class AsyncImportService extends BaseApiService {
+    /**
+     * Calculate SHA256 hash of a file
+     */
+    private calculateSHA256;
+    sdrfFile(request: MetadataImportRequest): Observable<AsyncTaskCreateResponse>;
+    excelFile(request: MetadataImportRequest): Observable<AsyncTaskCreateResponse>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<AsyncImportService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<AsyncImportService>;
+}
+
+declare class AsyncValidationService extends BaseApiService {
+    metadataTable(request: MetadataValidationRequest): Observable<AsyncTaskCreateResponse>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<AsyncValidationService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<AsyncValidationService>;
+}
+
+declare class ChunkedUploadService extends BaseApiService {
+    /**
+     * Initialize or continue a chunked upload
+     */
+    uploadChunk(request: ChunkedUploadRequest, uploadId?: string, offset?: number, totalSize?: number): Observable<ChunkedUploadResponse>;
+    /**
+     * Get chunked upload status
+     */
+    getUploadStatus(uploadId: string): Observable<ChunkedUploadStatus>;
+    /**
+     * Complete the chunked upload and process the file
+     */
+    completeUpload(uploadId: string, request?: ChunkedUploadCompletionRequest): Observable<ChunkedUploadCompletionResponse>;
+    /**
+     * Delete/cancel a chunked upload
+     */
+    cancelUpload(uploadId: string): Observable<void>;
+    /**
+     * Helper method to upload a file in chunks with progress tracking
+     */
+    uploadFileInChunks(file: File, chunkSize?: number, // 1MB chunks by default
+    options?: {
+        metadataTableId?: number;
+        createPools?: boolean;
+        replaceExisting?: boolean;
+        uploadSessionId?: string;
+        onProgress?: (progress: number) => void;
+    }): Observable<ChunkedUploadCompletionResponse>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<ChunkedUploadService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<ChunkedUploadService>;
+}
+
+declare class CupcakeVanilla {
+    static ɵfac: i0.ɵɵFactoryDeclaration<CupcakeVanilla, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<CupcakeVanilla, "ccv-cupcake-vanilla", never, {}, {}, never, never, true, never>;
+}
+
+export { AsyncExportService, AsyncImportService, AsyncTaskService, AsyncValidationService, ChunkedUploadService, CupcakeVanilla, FavouriteMetadataOptionService, MetadataColumnService, MetadataColumnTemplateService, MetadataColumnTemplateShareService, MetadataManagementService, MetadataTableService, MetadataTableTemplateService, OntologySearchService, OntologyType, OntologyTypeLabels, OntologyUtils, SDRFDefaultsService, SamplePoolService, SchemaService, TASK_STATUS_COLORS, TASK_STATUS_LABELS, TASK_TYPE_LABELS, TemplatePermissionLabels, TemplatePermissionLevel, isUnimodFullData };
+export type { ApiResponse, AsyncTaskCreateResponse, AsyncTaskQueryParams, AsyncTaskStatus, BaseTimestampedModel, BulkExcelExportRequest, BulkExportRequest, CellOntology, ChEBICompound, ChunkedUploadCompletionRequest, ChunkedUploadCompletionResponse, ChunkedUploadRequest, ChunkedUploadResponse, ChunkedUploadStatus, DownloadUrlResponse, FavouriteMetadataOption, FavouriteMetadataOptionCreateRequest, FavouriteMetadataOptionQueryParams, FavouriteMetadataOptionUpdateRequest, HumanDisease, MSUniqueVocabularies, MetadataColumn, MetadataColumnCreateRequest, MetadataColumnModifier, MetadataColumnQueryParams, MetadataColumnTemplate, MetadataColumnTemplateCreateRequest, MetadataColumnTemplateQueryParams, MetadataColumnTemplateShare, MetadataColumnTemplateShareCreateRequest, MetadataColumnTemplateShareQueryParams, MetadataColumnTemplateUpdateRequest, MetadataColumnUpdateRequest, MetadataExportRequest, MetadataImportRequest, MetadataQueryParams, MetadataTable, MetadataTableCreateRequest, MetadataTableQueryParams, MetadataTableQueryResponse, MetadataTableTemplate, MetadataTableTemplateCreateRequest, MetadataTableTemplateQueryParams, MetadataTableTemplateQueryResponse, MetadataTableTemplateUpdateRequest, MetadataTableUpdateRequest, MetadataValidationConfig, MetadataValidationRequest, MondoDisease, NCBITaxonomy, OntologySuggestion, OntologySuggestionResponse, PSIMSOntology, PaginatedResponse, SamplePool, SamplePoolCreateRequest, SamplePoolQueryParams, SamplePoolUpdateRequest, Schema, SchemaQueryParams, Species, SubcellularLocation, TaskListItem, TaskResult, TaskStatus, TaskType, Tissue, UberonAnatomy, Unimod, UnimodFullData, UnimodSpecification };