@noatgnu/cupcake-vanilla 1.0.0

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  1. package/README.md +63 -0
  2. package/fesm2022/noatgnu-cupcake-vanilla.mjs +1179 -0
  3. package/fesm2022/noatgnu-cupcake-vanilla.mjs.map +1 -0
  4. package/index.d.ts +1491 -0
  5. package/package.json +36 -0
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{"version":3,"file":"noatgnu-cupcake-vanilla.mjs","sources":["../../../projects/cupcake-vanilla/src/lib/models/enums.ts","../../../projects/cupcake-vanilla/src/lib/models/ontology-utils.ts","../../../projects/cupcake-vanilla/src/lib/models/async-task.ts","../../../projects/cupcake-vanilla/src/lib/services/metadata-table.ts","../../../projects/cupcake-vanilla/src/lib/services/metadata-column.ts","../../../projects/cupcake-vanilla/src/lib/services/sample-pool.ts","../../../projects/cupcake-vanilla/src/lib/services/metadata-table-template.ts","../../../projects/cupcake-vanilla/src/lib/services/favourite-metadata-option.ts","../../../projects/cupcake-vanilla/src/lib/services/metadata-column-template.ts","../../../projects/cupcake-vanilla/src/lib/services/metadata-column-template-share.ts","../../../projects/cupcake-vanilla/src/lib/services/metadata-management.ts","../../../projects/cupcake-vanilla/src/lib/services/ontology-search.ts","../../../projects/cupcake-vanilla/src/lib/services/schema.ts","../../../projects/cupcake-vanilla/src/lib/services/sdrf-defaults.ts","../../../projects/cupcake-vanilla/src/lib/services/async-task.ts","../../../projects/cupcake-vanilla/src/lib/services/async-export.ts","../../../projects/cupcake-vanilla/src/lib/services/async-import.ts","../../../projects/cupcake-vanilla/src/lib/services/async-validation.ts","../../../projects/cupcake-vanilla/src/lib/services/chunked-upload.ts","../../../projects/cupcake-vanilla/src/lib/cupcake-vanilla.ts","../../../projects/cupcake-vanilla/src/public-api.ts","../../../projects/cupcake-vanilla/src/noatgnu-cupcake-vanilla.ts"],"sourcesContent":["export enum OntologyType {\r\n SPECIES = 'species',\r\n TISSUE = 'tissue',\r\n HUMAN_DISEASE = 'human_disease',\r\n SUBCELLULAR_LOCATION = 'subcellular_location',\r\n UNIMOD = 'unimod',\r\n NCBI_TAXONOMY = 'ncbi_taxonomy',\r\n MONDO = 'mondo',\r\n UBERON = 'uberon',\r\n CHEBI = 'chebi',\r\n CELL_ONTOLOGY = 'cell_ontology',\r\n MS_UNIQUE_VOCABULARIES = 'ms_unique_vocabularies',\r\n PSI_MS = 'psi_ms'\r\n}\r\n\r\nexport const OntologyTypeLabels: Record<OntologyType, string> = {\r\n [OntologyType.SPECIES]: 'Species',\r\n [OntologyType.TISSUE]: 'Tissue',\r\n [OntologyType.HUMAN_DISEASE]: 'Human Disease',\r\n [OntologyType.SUBCELLULAR_LOCATION]: 'Subcellular Location',\r\n [OntologyType.UNIMOD]: 'Unimod Modifications',\r\n [OntologyType.NCBI_TAXONOMY]: 'NCBI Taxonomy',\r\n [OntologyType.MONDO]: 'MONDO Disease',\r\n [OntologyType.UBERON]: 'UBERON Anatomy',\r\n [OntologyType.CHEBI]: 'ChEBI',\r\n [OntologyType.CELL_ONTOLOGY]: 'Cell Ontology',\r\n [OntologyType.MS_UNIQUE_VOCABULARIES]: 'MS Unique Vocabularies',\r\n [OntologyType.PSI_MS]: 'PSI-MS Controlled Vocabulary'\r\n};\r\n\r\nexport enum TemplatePermissionLevel {\r\n READ = 'read',\r\n WRITE = 'write',\r\n ADMIN = 'admin'\r\n}\r\n\r\nexport const TemplatePermissionLabels: Record<TemplatePermissionLevel, string> = {\r\n [TemplatePermissionLevel.READ]: 'Read Only',\r\n [TemplatePermissionLevel.WRITE]: 'Read & Write',\r\n [TemplatePermissionLevel.ADMIN]: 'Administrator'\r\n};","export interface UnimodSpecification {\r\n accession: string;\r\n name: string;\r\n definition: string;\r\n additional_data: Array<{id: string; description: string}>;\r\n general_properties: Record<string, string>;\r\n specifications: Record<string, UnimodSpecification>;\r\n delta_mono_mass: string;\r\n delta_avge_mass: string;\r\n delta_composition: string;\r\n [key: string]: any;\r\n}\r\n\r\nexport interface UnimodFullData {\r\n accession: string;\r\n name: string;\r\n definition: string;\r\n additional_data: Array<{id: string; description: string}>;\r\n general_properties: Record<string, string>;\r\n specifications: Record<string, UnimodSpecification>;\r\n delta_mono_mass: string;\r\n delta_avge_mass: string;\r\n delta_composition: string;\r\n [key: string]: any;\r\n}\r\n\r\nexport function isUnimodFullData(suggestion: any): suggestion is { full_data: UnimodFullData } {\r\n return suggestion && \r\n suggestion.ontology_type === 'unimod' && \r\n !!suggestion.full_data;\r\n}\r\n\r\nexport class OntologyUtils {\r\n static getUnimodSpecifications(suggestion: any): (UnimodSpecification & { specNumber: string })[] {\r\n if (!isUnimodFullData(suggestion)) return [];\r\n \r\n return Object.entries(suggestion.full_data.specifications).map(([specNum, spec]) => ({\r\n ...spec,\r\n specNumber: specNum\r\n }));\r\n }\r\n\r\n static getActiveUnimodSpecifications(suggestion: any): (UnimodSpecification & { specNumber: string })[] {\r\n return this.getUnimodSpecifications(suggestion).filter(spec => !spec['hidden']);\r\n }\r\n\r\n static formatUnimodName(data: UnimodFullData): string {\r\n return `${data.name} (${data.accession})`;\r\n }\r\n}","// Task status and type definitions\r\nexport type TaskStatus = 'QUEUED' | 'STARTED' | 'SUCCESS' | 'FAILURE' | 'CANCELLED';\r\n\r\nexport type TaskType = \r\n | 'EXPORT_EXCEL' \r\n | 'EXPORT_SDRF' \r\n | 'IMPORT_SDRF' \r\n | 'IMPORT_EXCEL'\r\n | 'EXPORT_MULTIPLE_SDRF'\r\n | 'EXPORT_MULTIPLE_EXCEL'\r\n | 'VALIDATE_TABLE';\r\n\r\nexport interface AsyncTaskStatus {\r\n id: string;\r\n taskType: TaskType;\r\n status: TaskStatus;\r\n user: number;\r\n userUsername?: string;\r\n metadataTable?: number;\r\n metadataTableName?: string;\r\n taskTypeDisplay?: string;\r\n statusDisplay?: string;\r\n parameters?: any;\r\n result?: any;\r\n errorMessage?: string;\r\n traceback?: string;\r\n createdAt: string;\r\n startedAt?: string;\r\n completedAt?: string;\r\n rqJobId?: string;\r\n queueName?: string;\r\n progressCurrent?: number;\r\n progressTotal?: number;\r\n progressDescription?: string;\r\n duration?: number;\r\n progressPercentage?: number;\r\n}\r\n\r\nexport interface TaskListItem {\r\n id: string;\r\n taskType: TaskType;\r\n taskTypeDisplay: string;\r\n status: TaskStatus;\r\n statusDisplay: string;\r\n user: number;\r\n userUsername: string;\r\n metadataTable: number | null;\r\n metadataTableName: string | null;\r\n progressPercentage: number;\r\n progressDescription: string;\r\n createdAt: string;\r\n startedAt: string | null;\r\n completedAt: string | null;\r\n duration: number | null;\r\n errorMessage: string | null;\r\n}\r\n\r\nexport interface TaskResult {\r\n id: number;\r\n task: string;\r\n file?: string;\r\n fileName?: string;\r\n contentType?: string;\r\n fileSize?: number;\r\n expiresAt: string;\r\n downloadCount?: number;\r\n lastDownloadedAt?: string;\r\n createdAt: string;\r\n}\r\n\r\n// Async Task Request/Response Interfaces\r\nexport interface MetadataExportRequest {\r\n metadataTableId: number;\r\n includePools?: boolean;\r\n metadataColumnIds?: number[];\r\n sampleNumber?: number;\r\n exportFormat?: string;\r\n labGroupIds?: number[];\r\n}\r\n\r\nexport interface BulkExportRequest {\r\n metadataTableIds: number[];\r\n includePools?: boolean;\r\n validateSdrf?: boolean;\r\n}\r\n\r\nexport interface BulkExcelExportRequest extends BulkExportRequest {\r\n metadataColumnIds?: number[];\r\n labGroupIds?: number[];\r\n}\r\n\r\nexport interface MetadataImportRequest {\r\n metadataTableId: number;\r\n file: File;\r\n replaceExisting?: boolean;\r\n validateOntologies?: boolean;\r\n}\r\n\r\nexport interface MetadataValidationRequest {\r\n metadataTableId: number;\r\n validateSdrfFormat?: boolean;\r\n includePools?: boolean;\r\n}\r\n\r\nexport interface MetadataValidationConfig {\r\n metadataTableId: number;\r\n metadataTableName: string;\r\n}\r\n\r\nexport interface AsyncTaskCreateResponse {\r\n taskId: string;\r\n message: string;\r\n}\r\n\r\nexport interface DownloadUrlResponse {\r\n downloadUrl: string;\r\n filename: string;\r\n contentType: string;\r\n fileSize: number;\r\n expiresAt: string;\r\n expiresInHours: number;\r\n}\r\n\r\n// Query parameters for async tasks\r\nexport interface AsyncTaskQueryParams {\r\n taskType?: string;\r\n status?: string;\r\n metadataTable?: number;\r\n search?: string;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n// Helper constants\r\nexport const TASK_TYPE_LABELS: Record<TaskType, string> = {\r\n 'EXPORT_EXCEL': 'Export Excel Template',\r\n 'EXPORT_SDRF': 'Export SDRF File',\r\n 'IMPORT_SDRF': 'Import SDRF File',\r\n 'IMPORT_EXCEL': 'Import Excel File',\r\n 'EXPORT_MULTIPLE_SDRF': 'Export Multiple SDRF Files',\r\n 'EXPORT_MULTIPLE_EXCEL': 'Export Multiple Excel Templates',\r\n 'VALIDATE_TABLE': 'Validate Metadata Table',\r\n};\r\n\r\nexport const TASK_STATUS_LABELS: Record<TaskStatus, string> = {\r\n 'QUEUED': 'Queued',\r\n 'STARTED': 'In Progress',\r\n 'SUCCESS': 'Completed',\r\n 'FAILURE': 'Failed',\r\n 'CANCELLED': 'Cancelled',\r\n};\r\n\r\nexport const TASK_STATUS_COLORS: Record<TaskStatus, string> = {\r\n 'QUEUED': 'secondary',\r\n 'STARTED': 'primary',\r\n 'SUCCESS': 'success',\r\n 'FAILURE': 'danger',\r\n 'CANCELLED': 'warning',\r\n};","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n MetadataTable,\r\n MetadataTableCreateRequest,\r\n MetadataTableUpdateRequest,\r\n MetadataTableQueryResponse,\r\n MetadataColumn,\r\n PaginatedResponse\r\n} from '../models';\r\n\r\nexport interface MetadataTableQueryParams {\r\n search?: string;\r\n ownerId?: number;\r\n labGroupId?: number;\r\n isPublished?: boolean;\r\n isLocked?: boolean;\r\n showShared?: boolean;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class MetadataTableService extends BaseApiService {\r\n\r\n /**\r\n * Get all metadata tables with optional filtering\r\n */\r\n getMetadataTables(params?: MetadataTableQueryParams): Observable<MetadataTableQueryResponse> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<MetadataTableQueryResponse>(`${this.apiUrl}/metadata-tables/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a single metadata table by ID\r\n */\r\n getMetadataTable(id: number): Observable<MetadataTable> {\r\n return this.get<MetadataTable>(`${this.apiUrl}/metadata-tables/${id}/`);\r\n }\r\n\r\n /**\r\n * Create a new metadata table\r\n */\r\n createMetadataTable(table: MetadataTableCreateRequest): Observable<MetadataTable> {\r\n return this.post<MetadataTable>(`${this.apiUrl}/metadata-tables/`, table);\r\n }\r\n\r\n /**\r\n * Update an existing metadata table\r\n */\r\n updateMetadataTable(id: number, table: MetadataTableUpdateRequest): Observable<MetadataTable> {\r\n return this.put<MetadataTable>(`${this.apiUrl}/metadata-tables/${id}/`, table);\r\n }\r\n\r\n /**\r\n * Partially update a metadata table\r\n */\r\n patchMetadataTable(id: number, table: Partial<MetadataTableUpdateRequest>): Observable<MetadataTable> {\r\n return this.patch<MetadataTable>(`${this.apiUrl}/metadata-tables/${id}/`, table);\r\n }\r\n\r\n /**\r\n * Delete a metadata table\r\n */\r\n deleteMetadataTable(id: number): Observable<void> {\r\n return this.delete<void>(`${this.apiUrl}/metadata-tables/${id}/`);\r\n }\r\n\r\n /**\r\n * Add a column to the metadata table\r\n */\r\n addColumn(id: number, columnData: any, position?: number): Observable<{ message: string; column: MetadataColumn }> {\r\n return this.post<{ message: string; column: MetadataColumn }>(`${this.apiUrl}/metadata-tables/${id}/add_column/`, {\r\n column_data: columnData,\r\n position\r\n });\r\n }\r\n\r\n /**\r\n * Add a column with automatic reordering\r\n */\r\n addColumnWithAutoReorder(id: number, request: { columnData: any }): Observable<{ message: string; column: MetadataColumn; reordered: boolean; schemaIdsUsed: number[] }> {\r\n return this.post<{ message: string; column: MetadataColumn; reordered: boolean; schemaIdsUsed: number[] }>(`${this.apiUrl}/metadata-tables/${id}/add_column_with_auto_reorder/`, request);\r\n }\r\n\r\n /**\r\n * Remove a column from the metadata table\r\n */\r\n removeColumn(id: number, columnId: number): Observable<{ message: string }> {\r\n return this.post<{ message: string }>(`${this.apiUrl}/metadata-tables/${id}/remove_column/`, {\r\n column_id: columnId\r\n });\r\n }\r\n\r\n /**\r\n * Reorder a column in the metadata table\r\n */\r\n reorderColumn(id: number, columnId: number, newPosition: number): Observable<{ message: string }> {\r\n return this.post<{ message: string }>(`${this.apiUrl}/metadata-tables/${id}/reorder_column/`, {\r\n column_id: columnId,\r\n new_position: newPosition\r\n });\r\n }\r\n\r\n /**\r\n * Normalize column positions\r\n */\r\n normalizeColumnPositions(id: number): Observable<{ message: string }> {\r\n return this.post<{ message: string }>(`${this.apiUrl}/metadata-tables/${id}/normalize_column_positions/`, {});\r\n }\r\n\r\n /**\r\n * Get all tables (admin only)\r\n */\r\n getAdminAllTables(): Observable<MetadataTable[]> {\r\n return this.get<MetadataTable[]>(`${this.apiUrl}/metadata-tables/admin_all_tables/`);\r\n }\r\n\r\n /**\r\n * Search metadata tables\r\n */\r\n searchMetadataTables(query: string): Observable<MetadataTableQueryResponse> {\r\n return this.getMetadataTables({ search: query });\r\n }\r\n\r\n /**\r\n * Get metadata tables by owner\r\n */\r\n getMetadataTablesByOwner(ownerId: number): Observable<MetadataTableQueryResponse> {\r\n return this.getMetadataTables({ ownerId: ownerId });\r\n }\r\n\r\n /**\r\n * Get shared metadata tables\r\n */\r\n getSharedMetadataTables(): Observable<MetadataTableQueryResponse> {\r\n return this.getMetadataTables({ showShared: true });\r\n }\r\n\r\n /**\r\n * Combine columns column-wise\r\n */\r\n combineColumnwise(request: { columnIds: number[] }): Observable<{ message: string; combinedColumn: any }> {\r\n return this.post<{ message: string; combinedColumn: any }>(`${this.apiUrl}/metadata-tables/combine_columnwise/`, request);\r\n }\r\n\r\n /**\r\n * Combine columns row-wise\r\n */\r\n combineRowwise(request: { columnIds: number[] }): Observable<{ message: string; combinedColumn: any }> {\r\n return this.post<{ message: string; combinedColumn: any }>(`${this.apiUrl}/metadata-tables/combine_rowwise/`, request);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n MetadataColumn,\r\n MetadataColumnCreateRequest,\r\n MetadataColumnUpdateRequest,\r\n PaginatedResponse,\r\n OntologySuggestion\r\n} from '../models';\r\n\r\nexport interface MetadataColumnQueryParams {\r\n search?: string;\r\n metadataTableId?: number;\r\n type?: string;\r\n name?: string;\r\n hidden?: boolean;\r\n mandatory?: boolean;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class MetadataColumnService extends BaseApiService {\r\n\r\n /**\r\n * Get all metadata columns with optional filtering\r\n */\r\n getMetadataColumns(params?: MetadataColumnQueryParams): Observable<PaginatedResponse<MetadataColumn>> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<PaginatedResponse<MetadataColumn>>(`${this.apiUrl}/metadata-columns/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a single metadata column by ID\r\n */\r\n getMetadataColumn(id: number): Observable<MetadataColumn> {\r\n return this.get<MetadataColumn>(`${this.apiUrl}/metadata-columns/${id}/`);\r\n }\r\n\r\n /**\r\n * Create a new metadata column\r\n */\r\n createMetadataColumn(column: MetadataColumnCreateRequest): Observable<MetadataColumn> {\r\n return this.post<MetadataColumn>(`${this.apiUrl}/metadata-columns/`, column);\r\n }\r\n\r\n /**\r\n * Update an existing metadata column\r\n */\r\n updateMetadataColumn(id: number, column: MetadataColumnUpdateRequest): Observable<MetadataColumn> {\r\n return this.put<MetadataColumn>(`${this.apiUrl}/metadata-columns/${id}/`, column);\r\n }\r\n\r\n /**\r\n * Partially update a metadata column\r\n */\r\n patchMetadataColumn(id: number, column: Partial<MetadataColumnUpdateRequest>): Observable<MetadataColumn> {\r\n return this.patch<MetadataColumn>(`${this.apiUrl}/metadata-columns/${id}/`, column);\r\n }\r\n\r\n /**\r\n * Delete a metadata column\r\n */\r\n deleteMetadataColumn(id: number): Observable<void> {\r\n return this.delete<void>(`${this.apiUrl}/metadata-columns/${id}/`);\r\n }\r\n\r\n /**\r\n * Bulk create metadata columns\r\n */\r\n bulkCreate(request: { columns: MetadataColumnCreateRequest[] }): Observable<MetadataColumn[]> {\r\n return this.post<MetadataColumn[]>(`${this.apiUrl}/metadata-columns/bulk_create/`, request);\r\n }\r\n\r\n /**\r\n * Validate SDRF data\r\n */\r\n validateSdrfData(request: { metadataIds: number[]; sampleNumber?: number }): Observable<{ valid: boolean; errors: any[]; sampleCount: number }> {\r\n return this.post<{ valid: boolean; errors: any[]; sampleCount: number }>(`${this.apiUrl}/metadata-columns/validate_sdrf_data/`, request);\r\n }\r\n\r\n /**\r\n * Get ontology suggestions for a column\r\n */\r\n getOntologySuggestions(params: { \r\n columnId: number; \r\n search?: string; \r\n limit?: number; \r\n searchType?: 'icontains' | 'istartswith' | 'exact';\r\n }): Observable<{\r\n ontologyType: string;\r\n suggestions: OntologySuggestion[];\r\n searchTerm: string;\r\n searchType: string;\r\n limit: number;\r\n count: number;\r\n customFilters: any;\r\n hasMore: boolean;\r\n }> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get(`${this.apiUrl}/metadata-columns/ontology_suggestions/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Validate value against column's ontology\r\n */\r\n validateValue(id: number, request: { value: string }): Observable<{ valid: boolean; value: string; ontologyType: string; suggestions?: any[] }> {\r\n return this.post(`${this.apiUrl}/metadata-columns/${id}/validate_value/`, request);\r\n }\r\n\r\n /**\r\n * Update column value with automatic modifier calculation\r\n */\r\n updateColumnValue(id: number, request: { \r\n value: string; \r\n sampleIndices?: number[]; \r\n valueType?: 'default' | 'sample_specific' | 'replace_all';\r\n }): Observable<{\r\n message: string;\r\n column: MetadataColumn;\r\n changes: any;\r\n valueType: string;\r\n }> {\r\n return this.post(`${this.apiUrl}/metadata-columns/${id}/update_column_value/`, request);\r\n }\r\n\r\n /**\r\n * Apply automatic ontology mapping to a column\r\n */\r\n applyOntologyMapping(id: number): Observable<{ applied: boolean; ontologyType: string; message: string }> {\r\n return this.post(`${this.apiUrl}/metadata-columns/${id}/apply_ontology_mapping/`, {});\r\n }\r\n\r\n /**\r\n * Detect ontology type for given column name and type\r\n */\r\n detectOntologyType(params: { name: string; type: string }): Observable<{ columnName: string; columnType: string; detectedOntologyType: string }> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get(`${this.apiUrl}/metadata-columns/detect_ontology_type/`, { params: httpParams });\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n SamplePool,\r\n SamplePoolCreateRequest,\r\n SamplePoolUpdateRequest,\r\n MetadataColumn,\r\n PaginatedResponse\r\n} from '../models';\r\n\r\nexport interface SamplePoolQueryParams {\r\n search?: string;\r\n metadataTable?: number;\r\n isReference?: boolean;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class SamplePoolService extends BaseApiService {\r\n\r\n /**\r\n * Get all sample pools with optional filtering\r\n */\r\n getSamplePools(params?: SamplePoolQueryParams): Observable<PaginatedResponse<SamplePool>> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<PaginatedResponse<SamplePool>>(`${this.apiUrl}/sample-pools/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a single sample pool by ID\r\n */\r\n getSamplePool(id: number): Observable<SamplePool> {\r\n return this.get<SamplePool>(`${this.apiUrl}/sample-pools/${id}/`);\r\n }\r\n\r\n /**\r\n * Create a new sample pool\r\n */\r\n createSamplePool(pool: SamplePoolCreateRequest): Observable<SamplePool> {\r\n return this.post<SamplePool>(`${this.apiUrl}/sample-pools/`, pool);\r\n }\r\n\r\n /**\r\n * Update an existing sample pool\r\n */\r\n updateSamplePool(id: number, pool: SamplePoolUpdateRequest): Observable<SamplePool> {\r\n return this.put<SamplePool>(`${this.apiUrl}/sample-pools/${id}/`, pool);\r\n }\r\n\r\n /**\r\n * Partially update a sample pool\r\n */\r\n patchSamplePool(id: number, pool: Partial<SamplePoolUpdateRequest>): Observable<SamplePool> {\r\n return this.patch<SamplePool>(`${this.apiUrl}/sample-pools/${id}/`, pool);\r\n }\r\n\r\n /**\r\n * Delete a sample pool\r\n */\r\n deleteSamplePool(id: number): Observable<void> {\r\n return this.delete<void>(`${this.apiUrl}/sample-pools/${id}/`);\r\n }\r\n\r\n /**\r\n * Get metadata columns associated with this pool\r\n */\r\n getMetadataColumns(id: number): Observable<MetadataColumn[]> {\r\n return this.get<MetadataColumn[]>(`${this.apiUrl}/sample-pools/${id}/metadata_columns/`);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n MetadataTableTemplate,\r\n MetadataTableTemplateCreateRequest,\r\n MetadataTableTemplateUpdateRequest,\r\n MetadataTableTemplateQueryResponse,\r\n MetadataTable,\r\n MetadataColumn,\r\n Schema,\r\n PaginatedResponse\r\n} from '../models';\r\n\r\nexport interface MetadataTableTemplateQueryParams {\r\n search?: string;\r\n ownerId?: number;\r\n labGroupId?: number;\r\n visibility?: string;\r\n isDefault?: boolean;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class MetadataTableTemplateService extends BaseApiService {\r\n\r\n /**\r\n * Get all metadata table templates with optional filtering\r\n */\r\n getMetadataTableTemplates(params?: MetadataTableTemplateQueryParams): Observable<MetadataTableTemplateQueryResponse> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<MetadataTableTemplateQueryResponse>(`${this.apiUrl}/metadata-table-templates/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a single metadata table template by ID\r\n */\r\n getMetadataTableTemplate(id: number): Observable<MetadataTableTemplate> {\r\n return this.get<MetadataTableTemplate>(`${this.apiUrl}/metadata-table-templates/${id}/`);\r\n }\r\n\r\n /**\r\n * Create a new metadata table template\r\n */\r\n createMetadataTableTemplate(template: MetadataTableTemplateCreateRequest): Observable<MetadataTableTemplate> {\r\n return this.post<MetadataTableTemplate>(`${this.apiUrl}/metadata-table-templates/`, template);\r\n }\r\n\r\n /**\r\n * Update an existing metadata table template\r\n */\r\n updateMetadataTableTemplate(id: number, template: MetadataTableTemplateUpdateRequest): Observable<MetadataTableTemplate> {\r\n return this.put<MetadataTableTemplate>(`${this.apiUrl}/metadata-table-templates/${id}/`, template);\r\n }\r\n\r\n /**\r\n * Partially update a metadata table template\r\n */\r\n patchMetadataTableTemplate(id: number, template: Partial<MetadataTableTemplateUpdateRequest>): Observable<MetadataTableTemplate> {\r\n return this.patch<MetadataTableTemplate>(`${this.apiUrl}/metadata-table-templates/${id}/`, template);\r\n }\r\n\r\n /**\r\n * Delete a metadata table template\r\n */\r\n deleteMetadataTableTemplate(id: number): Observable<void> {\r\n return this.delete<void>(`${this.apiUrl}/metadata-table-templates/${id}/`);\r\n }\r\n\r\n /**\r\n * Add a column to the template\r\n */\r\n addColumn(id: number, request: { column_data: any; position?: number }): Observable<{ message: string; column: MetadataColumn }> {\r\n return this.post<{ message: string; column: MetadataColumn }>(`${this.apiUrl}/metadata-table-templates/${id}/add_column/`, request);\r\n }\r\n\r\n /**\r\n * Remove a column from the template\r\n */\r\n removeColumn(id: number, request: { column_id: number }): Observable<{ message: string }> {\r\n return this.post<{ message: string }>(`${this.apiUrl}/metadata-table-templates/${id}/remove_column/`, request);\r\n }\r\n\r\n /**\r\n * Reorder a column within the template\r\n */\r\n reorderColumn(id: number, request: { column_id: number; new_position: number }): Observable<{ message: string }> {\r\n return this.post<{ message: string }>(`${this.apiUrl}/metadata-table-templates/${id}/reorder_column/`, request);\r\n }\r\n\r\n /**\r\n * Add a column with automatic reordering\r\n */\r\n addColumnWithAutoReorder(id: number, request: { columnData: any }): Observable<{ message: string; column: MetadataColumn; reordered: boolean; schemaIdsUsed: number[] }> {\r\n return this.post<{ message: string; column: MetadataColumn; reordered: boolean; schemaIdsUsed: number[] }>(`${this.apiUrl}/metadata-table-templates/${id}/add_column_with_auto_reorder/`, request);\r\n }\r\n\r\n /**\r\n * Duplicate a column within the template\r\n */\r\n duplicateColumn(id: number, request: { column_id: number }): Observable<{ message: string; duplicated_column: MetadataColumn }> {\r\n return this.post<{ message: string; duplicated_column: MetadataColumn }>(`${this.apiUrl}/metadata-table-templates/${id}/duplicate_column/`, request);\r\n }\r\n\r\n /**\r\n * Normalize column positions\r\n */\r\n normalizeColumnPositions(id: number): Observable<{ message: string }> {\r\n return this.post<{ message: string }>(`${this.apiUrl}/metadata-table-templates/${id}/normalize_column_positions/`, {});\r\n }\r\n\r\n /**\r\n * Apply this template to a metadata table\r\n */\r\n applyToMetadataTable(id: number, request: { metadata_table_id: number }): Observable<{ message: string; applied_columns: MetadataColumn[] }> {\r\n return this.post<{ message: string; applied_columns: MetadataColumn[] }>(`${this.apiUrl}/metadata-table-templates/${id}/apply_to_metadata_table/`, request);\r\n }\r\n\r\n /**\r\n * Update field mask for template\r\n */\r\n updateFieldMask(id: number, request: { field_mask: any }): Observable<{ message: string; field_mask: any }> {\r\n return this.post<{ message: string; field_mask: any }>(`${this.apiUrl}/metadata-table-templates/${id}/update_field_mask/`, request);\r\n }\r\n\r\n /**\r\n * Get field mask for template\r\n */\r\n getFieldMask(id: number): Observable<{ field_mask: any }> {\r\n return this.get<{ field_mask: any }>(`${this.apiUrl}/metadata-table-templates/${id}/get_field_mask/`);\r\n }\r\n\r\n /**\r\n * Get columns with field masks\r\n */\r\n getColumnsWithFieldMasks(id: number): Observable<{ columns: any[] }> {\r\n return this.get<{ columns: any[] }>(`${this.apiUrl}/metadata-table-templates/${id}/get_columns_with_field_masks/`);\r\n }\r\n\r\n /**\r\n * Get available schemas for creating templates\r\n */\r\n getAvailableSchemas(): Observable<Schema[]> {\r\n return this.get<Schema[]>(`${this.apiUrl}/metadata-table-templates/available_schemas/`);\r\n }\r\n\r\n /**\r\n * Create a new template from schema definitions\r\n */\r\n createFromSchema(request: { schemaIds: number[]; name: string; description?: string }): Observable<{ message: string; template: MetadataTableTemplate }> {\r\n return this.post<{ message: string; template: MetadataTableTemplate }>(`${this.apiUrl}/metadata-table-templates/create_from_schema/`, request);\r\n }\r\n\r\n /**\r\n * Create a new metadata table from an existing template\r\n */\r\n createTableFromTemplate(request: { templateId: number; name: string; description?: string; sampleCount: number }): Observable<{ message: string; table: MetadataTable }> {\r\n return this.post<{ message: string; table: MetadataTable }>(`${this.apiUrl}/metadata-table-templates/create_table_from_template/`, request);\r\n }\r\n\r\n /**\r\n * Create a new metadata table directly from schema definitions\r\n */\r\n createTableFromSchemas(request: { schemaIds: number[]; name: string; description?: string; sampleCount: number }): Observable<{ message: string; table: MetadataTable }> {\r\n return this.post<{ message: string; table: MetadataTable }>(`${this.apiUrl}/metadata-table-templates/create_table_from_schemas/`, request);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n FavouriteMetadataOption,\r\n FavouriteMetadataOptionCreateRequest,\r\n FavouriteMetadataOptionUpdateRequest,\r\n PaginatedResponse\r\n} from '../models';\r\n\r\nexport interface FavouriteMetadataOptionQueryParams {\r\n search?: string;\r\n type?: string;\r\n userId?: number;\r\n labGroupId?: number;\r\n isGlobal?: boolean;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class FavouriteMetadataOptionService extends BaseApiService {\r\n\r\n /**\r\n * Get all favourite metadata options with optional filtering\r\n */\r\n getFavouriteMetadataOptions(params?: FavouriteMetadataOptionQueryParams): Observable<PaginatedResponse<FavouriteMetadataOption>> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<PaginatedResponse<FavouriteMetadataOption>>(`${this.apiUrl}/favourite-metadata-options/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a single favourite metadata option by ID\r\n */\r\n getFavouriteMetadataOption(id: number): Observable<FavouriteMetadataOption> {\r\n return this.get<FavouriteMetadataOption>(`${this.apiUrl}/favourite-metadata-options/${id}/`);\r\n }\r\n\r\n /**\r\n * Create a new favourite metadata option\r\n */\r\n createFavouriteMetadataOption(option: FavouriteMetadataOptionCreateRequest): Observable<FavouriteMetadataOption> {\r\n return this.post<FavouriteMetadataOption>(`${this.apiUrl}/favourite-metadata-options/`, option);\r\n }\r\n\r\n /**\r\n * Update an existing favourite metadata option\r\n */\r\n updateFavouriteMetadataOption(id: number, option: FavouriteMetadataOptionUpdateRequest): Observable<FavouriteMetadataOption> {\r\n return this.put<FavouriteMetadataOption>(`${this.apiUrl}/favourite-metadata-options/${id}/`, option);\r\n }\r\n\r\n /**\r\n * Partially update a favourite metadata option\r\n */\r\n patchFavouriteMetadataOption(id: number, option: Partial<FavouriteMetadataOptionUpdateRequest>): Observable<FavouriteMetadataOption> {\r\n return this.patch<FavouriteMetadataOption>(`${this.apiUrl}/favourite-metadata-options/${id}/`, option);\r\n }\r\n\r\n /**\r\n * Delete a favourite metadata option\r\n */\r\n deleteFavouriteMetadataOption(id: number): Observable<void> {\r\n return this.delete<void>(`${this.apiUrl}/favourite-metadata-options/${id}/`);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n MetadataColumnTemplate,\r\n MetadataColumnTemplateCreateRequest,\r\n MetadataColumnTemplateUpdateRequest,\r\n MetadataColumn,\r\n OntologySuggestion,\r\n PaginatedResponse\r\n} from '../models';\r\n\r\nexport interface MetadataColumnTemplateQueryParams {\r\n search?: string;\r\n type?: string;\r\n ontologyType?: string;\r\n isRequired?: boolean;\r\n isPublic?: boolean;\r\n ownerId?: number;\r\n labGroupId?: number;\r\n visibility?: string;\r\n isActive?: boolean;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class MetadataColumnTemplateService extends BaseApiService {\r\n\r\n /**\r\n * Get all metadata column templates with optional filtering\r\n */\r\n getMetadataColumnTemplates(params?: MetadataColumnTemplateQueryParams): Observable<PaginatedResponse<MetadataColumnTemplate>> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<PaginatedResponse<MetadataColumnTemplate>>(`${this.apiUrl}/metadata-column-templates/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a single metadata column template by ID\r\n */\r\n getMetadataColumnTemplate(id: number): Observable<MetadataColumnTemplate> {\r\n return this.get<MetadataColumnTemplate>(`${this.apiUrl}/metadata-column-templates/${id}/`);\r\n }\r\n\r\n /**\r\n * Create a new metadata column template\r\n */\r\n createMetadataColumnTemplate(template: MetadataColumnTemplateCreateRequest): Observable<MetadataColumnTemplate> {\r\n return this.post<MetadataColumnTemplate>(`${this.apiUrl}/metadata-column-templates/`, template);\r\n }\r\n\r\n /**\r\n * Update an existing metadata column template\r\n */\r\n updateMetadataColumnTemplate(id: number, template: MetadataColumnTemplateUpdateRequest): Observable<MetadataColumnTemplate> {\r\n return this.put<MetadataColumnTemplate>(`${this.apiUrl}/metadata-column-templates/${id}/`, template);\r\n }\r\n\r\n /**\r\n * Partially update a metadata column template\r\n */\r\n patchMetadataColumnTemplate(id: number, template: Partial<MetadataColumnTemplateUpdateRequest>): Observable<MetadataColumnTemplate> {\r\n return this.patch<MetadataColumnTemplate>(`${this.apiUrl}/metadata-column-templates/${id}/`, template);\r\n }\r\n\r\n /**\r\n * Delete a metadata column template\r\n */\r\n deleteMetadataColumnTemplate(id: number): Observable<void> {\r\n return this.delete<void>(`${this.apiUrl}/metadata-column-templates/${id}/`);\r\n }\r\n\r\n /**\r\n * Create a MetadataColumn from this template\r\n */\r\n createMetadataColumn(id: number, request: { metadataTableId: number; columnPosition?: number }): Observable<{ message: string; column: MetadataColumn }> {\r\n return this.post<{ message: string; column: MetadataColumn }>(`${this.apiUrl}/metadata-column-templates/${id}/create_metadata_column/`, request);\r\n }\r\n\r\n /**\r\n * Share this template with another user\r\n */\r\n shareTemplate(id: number, request: { userId: number; canEdit?: boolean }): Observable<{ message: string }> {\r\n return this.post<{ message: string }>(`${this.apiUrl}/metadata-column-templates/${id}/share_template/`, request);\r\n }\r\n\r\n /**\r\n * Remove template sharing for a user\r\n */\r\n unshareTemplate(id: number, request: { userId: number }): Observable<{ message: string }> {\r\n return this.delete<{ message: string }>(`${this.apiUrl}/metadata-column-templates/${id}/unshare_template/`, { body: request });\r\n }\r\n\r\n /**\r\n * Get templates created by the current user\r\n */\r\n getMyTemplates(): Observable<MetadataColumnTemplate[]> {\r\n return this.get<MetadataColumnTemplate[]>(`${this.apiUrl}/metadata-column-templates/my_templates/`);\r\n }\r\n\r\n /**\r\n * Get most popular public templates\r\n */\r\n getPopularTemplates(): Observable<MetadataColumnTemplate[]> {\r\n return this.get<MetadataColumnTemplate[]>(`${this.apiUrl}/metadata-column-templates/popular_templates/`);\r\n }\r\n\r\n /**\r\n * Get ontology suggestions for this column template\r\n */\r\n getOntologySuggestions(params?: { \r\n search?: string; \r\n templateId?: number;\r\n limit?: number;\r\n searchType?: 'icontains' | 'istartswith' | 'exact';\r\n }): Observable<{\r\n ontologyType: string;\r\n suggestions: OntologySuggestion[];\r\n searchTerm: string;\r\n searchType: string;\r\n limit: number;\r\n count: number;\r\n customFilters: any;\r\n hasMore: boolean;\r\n }> {\r\n const httpParams = this.buildHttpParams({\r\n template_id: params?.templateId,\r\n search: params?.search,\r\n limit: params?.limit,\r\n search_type: params?.searchType\r\n });\r\n return this.get<{\r\n ontologyType: string;\r\n suggestions: OntologySuggestion[];\r\n searchTerm: string;\r\n searchType: string;\r\n limit: number;\r\n count: number;\r\n customFilters: any;\r\n hasMore: boolean;\r\n }>(`${this.apiUrl}/metadata-column-templates/ontology_suggestions/`, { params: httpParams });\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n MetadataColumnTemplateShare,\r\n MetadataColumnTemplateShareCreateRequest,\r\n PaginatedResponse\r\n} from '../models';\r\n\r\nexport interface MetadataColumnTemplateShareQueryParams {\r\n template?: number;\r\n sharedWith?: number;\r\n sharedBy?: number;\r\n canEdit?: boolean;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class MetadataColumnTemplateShareService extends BaseApiService {\r\n\r\n /**\r\n * Get all template shares with optional filtering\r\n */\r\n getMetadataColumnTemplateShares(params?: MetadataColumnTemplateShareQueryParams): Observable<PaginatedResponse<MetadataColumnTemplateShare>> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<PaginatedResponse<MetadataColumnTemplateShare>>(`${this.apiUrl}/metadata-column-template-shares/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a single template share by ID\r\n */\r\n getMetadataColumnTemplateShare(id: number): Observable<MetadataColumnTemplateShare> {\r\n return this.get<MetadataColumnTemplateShare>(`${this.apiUrl}/metadata-column-template-shares/${id}/`);\r\n }\r\n\r\n /**\r\n * Create a new template share\r\n */\r\n createMetadataColumnTemplateShare(share: MetadataColumnTemplateShareCreateRequest): Observable<MetadataColumnTemplateShare> {\r\n return this.post<MetadataColumnTemplateShare>(`${this.apiUrl}/metadata-column-template-shares/`, share);\r\n }\r\n\r\n /**\r\n * Update an existing template share\r\n */\r\n updateMetadataColumnTemplateShare(id: number, share: { canEdit?: boolean }): Observable<MetadataColumnTemplateShare> {\r\n return this.put<MetadataColumnTemplateShare>(`${this.apiUrl}/metadata-column-template-shares/${id}/`, share);\r\n }\r\n\r\n /**\r\n * Delete a template share\r\n */\r\n deleteMetadataColumnTemplateShare(id: number): Observable<void> {\r\n return this.delete<void>(`${this.apiUrl}/metadata-column-template-shares/${id}/`);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class MetadataManagementService extends BaseApiService {\r\n\r\n /**\r\n * Export metadata as Excel template (matching original CUPCAKE)\r\n */\r\n exportExcelTemplate(request: any): Observable<Blob> {\r\n return this.post(`${this.apiUrl}/metadata-management/export_excel_template/`, request, { responseType: 'blob' });\r\n }\r\n\r\n /**\r\n * Import metadata from SDRF file with intelligent column matching and schema organization\r\n */\r\n importSdrfFile(file: File, additionalData?: any): Observable<any> {\r\n const formData = new FormData();\r\n formData.append('file', file);\r\n if (additionalData) {\r\n Object.keys(additionalData).forEach(key => {\r\n formData.append(key, additionalData[key]);\r\n });\r\n }\r\n return this.post<any>(`${this.apiUrl}/metadata-management/import_sdrf_file/`, formData);\r\n }\r\n\r\n /**\r\n * Import metadata from Excel file (matching original CUPCAKE)\r\n */\r\n importExcelFile(file: File, additionalData?: any): Observable<any> {\r\n const formData = new FormData();\r\n formData.append('file', file);\r\n if (additionalData) {\r\n Object.keys(additionalData).forEach(key => {\r\n formData.append(key, additionalData[key]);\r\n });\r\n }\r\n return this.post<any>(`${this.apiUrl}/metadata-management/import_excel_file/`, formData);\r\n }\r\n\r\n /**\r\n * Collect metadata from metadata table\r\n */\r\n collectMetadata(params: any): Observable<any> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<any>(`${this.apiUrl}/metadata-management/collect_metadata/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Export metadata as SDRF file (matching original CUPCAKE)\r\n */\r\n exportSdrfFile(request: any): Observable<Blob> {\r\n return this.post(`${this.apiUrl}/metadata-management/export_sdrf_file/`, request, { responseType: 'blob' });\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n OntologySuggestion\r\n} from '../models';\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class OntologySearchService extends BaseApiService {\r\n\r\n /**\r\n * Get ontology suggestions across all sources for SDRF validation\r\n */\r\n suggest(params?: { query?: string; sources?: string[] }): Observable<OntologySuggestion[]> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<OntologySuggestion[]>(`${this.apiUrl}/ontology-search/suggest/`, { params: httpParams });\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n Schema,\r\n PaginatedResponse\r\n} from '../models';\r\n\r\nexport interface SchemaQueryParams {\r\n search?: string;\r\n category?: string;\r\n isActive?: boolean;\r\n limit?: number;\r\n offset?: number;\r\n ordering?: string;\r\n}\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class SchemaService extends BaseApiService {\r\n\r\n /**\r\n * Get all schemas with optional filtering\r\n */\r\n getSchemas(params?: SchemaQueryParams): Observable<PaginatedResponse<Schema>> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<PaginatedResponse<Schema>>(`${this.apiUrl}/schemas/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a single schema by ID\r\n */\r\n getSchema(id: number): Observable<Schema> {\r\n return this.get<Schema>(`${this.apiUrl}/schemas/${id}/`);\r\n }\r\n\r\n /**\r\n * Get list of available schemas for creating templates\r\n */\r\n getAvailableSchemas(): Observable<Schema[]> {\r\n return this.get<Schema[]>(`${this.apiUrl}/schemas/available/`);\r\n }\r\n\r\n /**\r\n * Sync builtin schemas from sdrf-pipelines package (admin only)\r\n */\r\n syncBuiltin(): Observable<{ message: string; synced_count: number }> {\r\n return this.post<{ message: string; synced_count: number }>(`${this.apiUrl}/schemas/sync_builtin/`, {});\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class SDRFDefaultsService extends BaseApiService {\r\n\r\n /**\r\n * Get all available SDRF columns with their default values\r\n */\r\n getColumns(): Observable<any[]> {\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/columns/`);\r\n }\r\n\r\n /**\r\n * Get default values for a specific column\r\n */\r\n getColumnValues(params: { column: string }): Observable<any[]> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/column_values/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Search for columns containing the query string\r\n */\r\n searchColumns(params: { query: string }): Observable<any[]> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/search/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get options for structured fields (key-value pairs)\r\n */\r\n getStructuredOptions(params: { field: string }): Observable<any[]> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/structured_options/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get all label options (TMT, SILAC, label-free)\r\n */\r\n getLabels(): Observable<any[]> {\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/labels/`);\r\n }\r\n\r\n /**\r\n * Get protein modification options (fixed and variable)\r\n */\r\n getModifications(): Observable<any[]> {\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/modifications/`);\r\n }\r\n\r\n /**\r\n * Get list of common instrument models\r\n */\r\n getInstruments(): Observable<any[]> {\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/instruments/`);\r\n }\r\n\r\n /**\r\n * Get cleavage agent options\r\n */\r\n getCleavageAgents(): Observable<any[]> {\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/cleavage_agents/`);\r\n }\r\n\r\n /**\r\n * Get all compound fields that require special handling\r\n */\r\n getCompoundFields(): Observable<any[]> {\r\n return this.get<any[]>(`${this.apiUrl}/sdrf-defaults/compound_fields/`);\r\n }\r\n\r\n /**\r\n * Get schema for a specific compound field\r\n */\r\n getCompoundSchema(params: { field: string }): Observable<any> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<any>(`${this.apiUrl}/sdrf-defaults/compound_schema/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Validate a compound field value against its schema\r\n */\r\n validateCompound(request: { field: string; value: any }): Observable<{ valid: boolean; errors?: string[] }> {\r\n return this.post<{ valid: boolean; errors?: string[] }>(`${this.apiUrl}/sdrf-defaults/validate_compound/`, request);\r\n }\r\n\r\n /**\r\n * Get column name suggestions based on partial input\r\n */\r\n getSuggestions(params: { query: string }): Observable<string[]> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<string[]>(`${this.apiUrl}/sdrf-defaults/suggestions/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get quick access to commonly used value categories\r\n */\r\n getQuickValues(): Observable<any> {\r\n return this.get<any>(`${this.apiUrl}/sdrf-defaults/quick_values/`);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n AsyncTaskStatus,\r\n AsyncTaskQueryParams,\r\n AsyncTaskCreateResponse,\r\n DownloadUrlResponse,\r\n PaginatedResponse\r\n} from '../models';\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class AsyncTaskService extends BaseApiService {\r\n\r\n /**\r\n * Get all async tasks for the current user with optional filtering\r\n */\r\n getAsyncTasks(params?: AsyncTaskQueryParams): Observable<PaginatedResponse<AsyncTaskStatus>> {\r\n const httpParams = this.buildHttpParams(params);\r\n return this.get<PaginatedResponse<AsyncTaskStatus>>(`${this.apiUrl}/async-tasks/`, { params: httpParams });\r\n }\r\n\r\n /**\r\n * Get a specific async task by ID\r\n */\r\n getAsyncTask(id: string): Observable<AsyncTaskStatus> {\r\n return this.get<AsyncTaskStatus>(`${this.apiUrl}/async-tasks/${id}/`);\r\n }\r\n\r\n /**\r\n * Cancel a queued or running task\r\n */\r\n cancelTask(id: string): Observable<{ message: string }> {\r\n return this.delete<{ message: string }>(`${this.apiUrl}/async-tasks/${id}/cancel/`);\r\n }\r\n\r\n /**\r\n * Generate a signed download URL for task result file\r\n */\r\n getDownloadUrl(id: string): Observable<DownloadUrlResponse> {\r\n return this.get<DownloadUrlResponse>(`${this.apiUrl}/async-tasks/${id}/download_url/`);\r\n }\r\n\r\n /**\r\n * Direct download endpoint (returns blob for file download)\r\n */\r\n downloadTaskFile(id: string, token: string): Observable<Blob> {\r\n const httpParams = this.buildHttpParams({ token });\r\n return this.get(`${this.apiUrl}/async-tasks/${id}/download/`, { params: httpParams, responseType: 'blob' });\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n MetadataExportRequest,\r\n BulkExportRequest,\r\n BulkExcelExportRequest,\r\n AsyncTaskCreateResponse\r\n} from '../models';\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class AsyncExportService extends BaseApiService {\r\n\r\n excelTemplate(request: MetadataExportRequest): Observable<AsyncTaskCreateResponse> {\r\n return this.post<AsyncTaskCreateResponse>(`${this.apiUrl}/async-export/excel_template/`, request);\r\n }\r\n\r\n sdrfFile(request: MetadataExportRequest): Observable<AsyncTaskCreateResponse> {\r\n return this.post<AsyncTaskCreateResponse>(`${this.apiUrl}/async-export/sdrf_file/`, request);\r\n }\r\n\r\n multipleSdrfFiles(request: BulkExportRequest): Observable<AsyncTaskCreateResponse> {\r\n return this.post<AsyncTaskCreateResponse>(`${this.apiUrl}/async-export/multiple_sdrf_files/`, request);\r\n }\r\n\r\n multipleExcelTemplates(request: BulkExcelExportRequest): Observable<AsyncTaskCreateResponse> {\r\n return this.post<AsyncTaskCreateResponse>(`${this.apiUrl}/async-export/multiple_excel_templates/`, request);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable, from } from 'rxjs';\r\nimport { switchMap } from 'rxjs/operators';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n MetadataImportRequest,\r\n AsyncTaskCreateResponse\r\n} from '../models';\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class AsyncImportService extends BaseApiService {\r\n\r\n /**\r\n * Calculate SHA256 hash of a file\r\n */\r\n private async calculateSHA256(file: File): Promise<string> {\r\n const buffer = await file.arrayBuffer();\r\n const hashBuffer = await crypto.subtle.digest('SHA-256', buffer);\r\n const hashArray = Array.from(new Uint8Array(hashBuffer));\r\n const hashHex = hashArray.map(b => b.toString(16).padStart(2, '0')).join('');\r\n return hashHex;\r\n }\r\n\r\n sdrfFile(request: MetadataImportRequest): Observable<AsyncTaskCreateResponse> {\r\n return from(this.calculateSHA256(request.file)).pipe(\r\n switchMap(sha256Hash => {\r\n const formData = new FormData();\r\n formData.append('metadata_table_id', request.metadataTableId.toString());\r\n formData.append('file', request.file);\r\n formData.append('sha256', sha256Hash);\r\n \r\n if (request.replaceExisting !== undefined) {\r\n formData.append('replace_existing', request.replaceExisting.toString());\r\n }\r\n if (request.validateOntologies !== undefined) {\r\n formData.append('validate_ontologies', request.validateOntologies.toString());\r\n }\r\n\r\n return this.post<AsyncTaskCreateResponse>(`${this.apiUrl}/async-import/sdrf_file/`, formData);\r\n })\r\n );\r\n }\r\n\r\n excelFile(request: MetadataImportRequest): Observable<AsyncTaskCreateResponse> {\r\n const formData = new FormData();\r\n formData.append('metadata_table_id', request.metadataTableId.toString());\r\n formData.append('file', request.file);\r\n \r\n if (request.replaceExisting !== undefined) {\r\n formData.append('replace_existing', request.replaceExisting.toString());\r\n }\r\n if (request.validateOntologies !== undefined) {\r\n formData.append('validate_ontologies', request.validateOntologies.toString());\r\n }\r\n\r\n return this.post<AsyncTaskCreateResponse>(`${this.apiUrl}/async-import/excel_file/`, formData);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable } from 'rxjs';\r\nimport { BaseApiService } from '@cupcake/core';\r\n\r\nimport {\r\n MetadataValidationRequest,\r\n AsyncTaskCreateResponse\r\n} from '../models';\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class AsyncValidationService extends BaseApiService {\r\n\r\n metadataTable(request: MetadataValidationRequest): Observable<AsyncTaskCreateResponse> {\r\n return this.post<AsyncTaskCreateResponse>(`${this.apiUrl}/async-validation/metadata_table/`, request);\r\n }\r\n}","import { Injectable } from '@angular/core';\r\nimport { Observable, from } from 'rxjs';\r\nimport { switchMap } from 'rxjs/operators';\r\nimport { BaseApiService } from '@cupcake/core';\r\nimport jsSHA from 'jssha';\r\n\r\nimport {\r\n ChunkedUploadStatus,\r\n ChunkedUploadRequest,\r\n ChunkedUploadResponse,\r\n ChunkedUploadCompletionRequest,\r\n ChunkedUploadCompletionResponse\r\n} from '../models';\r\n\r\n@Injectable({\r\n providedIn: 'root'\r\n})\r\nexport class ChunkedUploadService extends BaseApiService {\r\n\r\n\r\n /**\r\n * Initialize or continue a chunked upload\r\n */\r\n uploadChunk(\r\n request: ChunkedUploadRequest, \r\n uploadId?: string,\r\n offset?: number,\r\n totalSize?: number\r\n ): Observable<ChunkedUploadResponse> {\r\n const formData = new FormData();\r\n formData.append('file', request.file);\r\n \r\n if (request.filename) {\r\n formData.append('filename', request.filename);\r\n }\r\n if (request.uploadSessionId) {\r\n formData.append('upload_session_id', request.uploadSessionId);\r\n }\r\n if (request.metadataTableId) {\r\n formData.append('metadata_table_id', request.metadataTableId.toString());\r\n }\r\n if (request.createPools !== undefined) {\r\n formData.append('create_pools', request.createPools.toString());\r\n }\r\n if (request.replaceExisting !== undefined) {\r\n formData.append('replace_existing', request.replaceExisting.toString());\r\n }\r\n\r\n const url = uploadId \r\n ? `${this.apiUrl}/chunked-upload/${uploadId}/`\r\n : `${this.apiUrl}/chunked-upload/`;\r\n\r\n // Add Content-Range header for chunked uploads\r\n const headers: any = {};\r\n if (offset !== undefined && totalSize !== undefined) {\r\n const chunkEnd = offset + request.file.size - 1;\r\n headers['Content-Range'] = `bytes ${offset}-${chunkEnd}/${totalSize}`;\r\n }\r\n\r\n // Use POST for first chunk, PUT for subsequent chunks\r\n if (uploadId) {\r\n return this.put<ChunkedUploadResponse>(url, formData, { headers });\r\n } else {\r\n return this.post<ChunkedUploadResponse>(url, formData, { headers });\r\n }\r\n }\r\n\r\n /**\r\n * Get chunked upload status\r\n */\r\n getUploadStatus(uploadId: string): Observable<ChunkedUploadStatus> {\r\n return this.get<ChunkedUploadStatus>(`${this.apiUrl}/chunked-upload/${uploadId}/`);\r\n }\r\n\r\n /**\r\n * Complete the chunked upload and process the file\r\n */\r\n completeUpload(uploadId: string, request?: ChunkedUploadCompletionRequest): Observable<ChunkedUploadCompletionResponse> {\r\n const formData = new FormData();\r\n \r\n if (request?.sha256) {\r\n formData.append('sha256', request.sha256);\r\n }\r\n if (request?.metadataTableId) {\r\n formData.append('metadata_table_id', request.metadataTableId.toString());\r\n }\r\n if (request?.createPools !== undefined) {\r\n formData.append('create_pools', request.createPools.toString());\r\n }\r\n if (request?.replaceExisting !== undefined) {\r\n formData.append('replace_existing', request.replaceExisting.toString());\r\n }\r\n\r\n return this.post<ChunkedUploadCompletionResponse>(`${this.apiUrl}/chunked-upload/${uploadId}/`, formData);\r\n }\r\n\r\n /**\r\n * Delete/cancel a chunked upload\r\n */\r\n cancelUpload(uploadId: string): Observable<void> {\r\n return this.delete<void>(`${this.apiUrl}/chunked-upload/${uploadId}/`);\r\n }\r\n\r\n /**\r\n * Helper method to upload a file in chunks with progress tracking\r\n */\r\n uploadFileInChunks(\r\n file: File, \r\n chunkSize: number = 1024 * 1024, // 1MB chunks by default\r\n options?: {\r\n metadataTableId?: number;\r\n createPools?: boolean;\r\n replaceExisting?: boolean;\r\n uploadSessionId?: string;\r\n onProgress?: (progress: number) => void;\r\n }\r\n ): Observable<ChunkedUploadCompletionResponse> {\r\n return new Observable(subscriber => {\r\n let uploadId: string | undefined;\r\n let offset = 0;\r\n const totalSize = file.size;\r\n const sha256 = new jsSHA('SHA-256', 'ARRAYBUFFER');\r\n \r\n const uploadNextChunk = () => {\r\n if (offset >= totalSize) {\r\n // Upload complete, finalize with calculated hash\r\n if (uploadId) {\r\n const calculatedHash = sha256.getHash('HEX');\r\n this.completeUpload(uploadId, {\r\n sha256: calculatedHash,\r\n metadataTableId: options?.metadataTableId,\r\n createPools: options?.createPools,\r\n replaceExisting: options?.replaceExisting\r\n }).subscribe({\r\n next: (result) => {\r\n subscriber.next(result);\r\n subscriber.complete();\r\n },\r\n error: (error) => subscriber.error(error)\r\n });\r\n } else {\r\n subscriber.error(new Error('Upload failed: No upload ID'));\r\n }\r\n return;\r\n }\r\n\r\n const end = Math.min(offset + chunkSize, totalSize);\r\n const chunk = file.slice(offset, end);\r\n const chunkFile = new File([chunk], file.name, { type: file.type });\r\n\r\n // Add chunk to hash calculation\r\n chunk.arrayBuffer().then(arrayBuffer => {\r\n sha256.update(arrayBuffer);\r\n \r\n this.uploadChunk({\r\n file: chunkFile,\r\n filename: file.name,\r\n uploadSessionId: options?.uploadSessionId,\r\n metadataTableId: options?.metadataTableId,\r\n createPools: options?.createPools,\r\n replaceExisting: options?.replaceExisting\r\n }, uploadId, offset, totalSize).subscribe({\r\n next: (response) => {\r\n uploadId = response.id;\r\n offset = response.offset;\r\n \r\n // Report progress\r\n const progress = (offset / totalSize) * 100;\r\n if (options?.onProgress) {\r\n options.onProgress(progress);\r\n }\r\n\r\n // Upload next chunk\r\n uploadNextChunk();\r\n },\r\n error: (error) => subscriber.error(error)\r\n });\r\n }).catch(error => subscriber.error(error));\r\n };\r\n\r\n uploadNextChunk();\r\n });\r\n }\r\n}","export * from './models';\nexport * from './services';\n\nimport { Component } from '@angular/core';\n\n@Component({\n selector: 'ccv-cupcake-vanilla',\n imports: [],\n template: `\n <p>\n cupcake-vanilla works!\n </p>\n `,\n styles: ``\n})\nexport class CupcakeVanilla {\n\n}\n","/*\n * Public API Surface of cupcake-vanilla\n */\n\nexport * from './lib/cupcake-vanilla';\nexport * from './lib/models';\n","/**\n * Generated bundle index. Do not edit.\n */\n\nexport * from 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