@cirrobio/sdk 0.10.5 → 0.10.6

package/dist/index.esm.js

@@ -271,7 +271,8 @@ function uploadFile({ bucket, path, file, credentials, metadata }) {
         Key: path,
         Body: file,
         ContentType: file.type,
-        Metadata: metadata
+        Metadata: metadata,
+        ChecksumType: "FULL_OBJECT"
     };
     return new Upload({
         client: createS3Client(credentials),

package/dist/index.esm.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.esm.js","sources":["../src/file/extensions.fn.ts","../src/file/util/credentials-mutex.so.ts","../src/file/util/s3-client.ts","../src/file/util/s3-utils.ts","../src/file/actions/sign-url.fn.ts","../src/util/get-resource-name.ts","../src/file/shared.ts","../src/file/file.service.ts","../src/file/actions/delete.fn.ts","../src/file/actions/upload.fn.ts","../src/file/project-access-context.ts","../src/file/models/file-object.model.ts","../src/file/calculate-size.ts","../src/formatters/json-pretty-print.ts","../src/formatters/bytes-to-string.ts","../src/formatters/normalize-date.ts","../src/formatters/normalize-string.ts","../src/formatters/slash.ts","../src/formatters/to-date-format.ts","../src/formatters/to-title-case.ts","../src/formatters/to-friendly-name.ts","../src/formatters/to-money.ts","../src/formatters/to-pascal-case.ts","../src/file/models/assets.ts","../src/file/models/folder.ts","../src/file/models/file.ts","../src/file/manifest-parser.ts","../src/file/util/get-parent.fn.ts","../src/api/error.ts","../src/api/error-handler.ts","../src/api/config.ts","../src/auth/current-user.ts","../src/auth/static-token-auth.ts","../src/data/data.service.ts","../src/util/extract-from-object.ts","../src/util/handle-promise.ts","../src/util/download.ts"],"sourcesContent":["\n/**\n * An array of file extensions that can be rendered in a genome viewer\n */\nexport const FILE_TRACK_ANNOTATION = ['bed', 'bed.gz', 'gtf', 'gtf.gz'];\nexport const FILE_TRACK_ALIGNMENTS = ['cram', 'cram.gz'];  // TODO: put back bam\nexport const FILE_TRACK_VARIANT = ['vcf', 'vcf.gz'];\nexport const FILE_TRACK_WIG = ['wig', 'wig.gz', 'bw', 'bw.gz', 'bigwig', 'bigwig.gz'];\nexport const FILE_TRACK_SEG = ['seg', 'seg.gz'];\nexport const FILE_TRACK_INDEX_EXTENSIONS = ['tbi', 'bai', 'crai', 'csi'];\nexport const FILE_VITESSCE_EXTENSIONS = ['hdf5', 'h5ad', 'loom'];\nexport const FILE_TRACK_EXTENSIONS_NO_INDEX = [\n    ...FILE_TRACK_ANNOTATION,\n    ...FILE_TRACK_ALIGNMENTS,\n    ...FILE_TRACK_VARIANT,\n    ...FILE_TRACK_WIG,\n    ...FILE_TRACK_SEG\n];\nexport const FILE_TRACK_EXTENSIONS = [\n    ...FILE_TRACK_EXTENSIONS_NO_INDEX,\n    ...FILE_TRACK_INDEX_EXTENSIONS\n]\n\n\nexport const FILE_BROWSER_EXTENSIONS = ['html', 'pdf'];\n\n\n/**\n * An array of file extensions that are protein structure files.\n */\nexport const FILE_PROTEIN_STRUCTURE_EXTENSIONS = ['pdb', 'pdb.gz', 'cif', 'cif.gz', 'ent', 'ent.gz', 'mmtf', 'mmtf.gz'];\n/**\n * An array of file extensions that are considered tabular files.\n */\nexport const FILE_DSV_EXTENSIONS = ['tab', 'csv', 'tsv', 'dsv'];\n/**\n * An array of file extensions that contain genomic sequence content.\n */\nexport const FILE_TXT_GENOMICS_EXTENSIONS = ['fasta', 'fna', 'fsa', 'fa', 'fastp', 'fastq', 'faa', 'gbk', 'gff', 'vcf', 'seq'];\n\n/**\n * An array of file extensions that are considered TXT files.\n */\nexport const FILE_TXT_EXTENSIONS = ['txt', 'log', 'yml', 'cfg', 'config', 'xml', 'yaml', ...FILE_DSV_EXTENSIONS, ...FILE_TXT_GENOMICS_EXTENSIONS];\n\n\n/**\n * An array of file extensions that are considered image files.\n */\nexport const FILE_IMAGE_EXTENSIONS = ['jpg', 'jpeg', 'png', 'svg'];\n\n/**\n * An array of file extensions that are considered OME (Open Microscopy Environment) files.\n */\nexport const FILE_OME_EXTENSIONS = ['tif', 'ome.tif', 'ome.tiff', 'ome.tif.gz', 'ome.tiff.gz'];\n\n/**\n * An array of file extensions that can be opened in the browser.\n * Includes common document formats such as HTML, PDF, and JSON, as well as image, DSV, TXT, and OME file formats.\n */\nexport const FILE_EXTENSIONS_TO_OPEN = ['html', 'pdf', 'json', 'fcs',\n    ...FILE_IMAGE_EXTENSIONS,\n    ...FILE_TXT_EXTENSIONS,\n    ...FILE_TRACK_EXTENSIONS,\n    ...FILE_PROTEIN_STRUCTURE_EXTENSIONS\n];\n\n\n/**\n * Checks if a file has an extension that matches one in the provided list.\n * @param filePath The file to check the extension of.\n * @param extensions A list of file endings to check the file against.\n * @returns True or false if the file has an ending in the extensions list.\n */\nexport function matchesExtension(filePath: string, extensions: string[]): boolean {\n    filePath = filePath.toLowerCase();\n\n    // Decompress the filePath if it ends with .gz\n    if (filePath.endsWith('.gz')) {\n        filePath = filePath.slice(0, -3);  // remove the .gz extension\n    }\n\n    // Now, get the extension of the file\n    const fileExtension = filePath.slice(filePath.lastIndexOf('.') + 1);\n\n    // Check if the fileExtension is in the list of extensions\n    return extensions.includes(fileExtension);\n}\n","import { AWSCredentials } from '@cirrobio/api-client';\n\nclass Mutex<T> {\n  private mutex = Promise.resolve();\n\n  lock(): PromiseLike<() => void> {\n    let begin: (unlock: () => void) => void = () => { /* Do nothing */ };\n\n    this.mutex = this.mutex.then(() => new Promise(begin));\n\n    return new Promise((res) => {\n      begin = res;\n    });\n  }\n\n  async dispatch(fn: (() => T) | (() => PromiseLike<T>)): Promise<T> {\n    const unlock = await this.lock();\n    try {\n      return await Promise.resolve(fn());\n    } finally {\n      unlock();\n    }\n  }\n}\n\n/**\n * A mutex to ensure that only one request for credentials is made at a time.\n */\nexport const credentialsMutex = new Mutex<AWSCredentials>();\n/**\n * A cache of credentials to avoid making multiple requests for the same credentials.\n */\nexport const credentialsCache: Map<string, AWSCredentials> = new Map<string, AWSCredentials>();\n","import { S3Client } from \"@aws-sdk/client-s3\";\nimport { AWSCredentials } from \"@cirrobio/api-client\";\n\nconst clientCache = new Map<string, S3Client>();\n\n/**\n * Creates an S3 client using the provided credentials.\n */\nexport function createS3Client(credentials: AWSCredentials): S3Client {\n  const cacheKey = `${credentials.accessKeyId}-${credentials.region}`;\n  const cachedClient = clientCache.get(cacheKey);\n  if (cachedClient) {\n    return cachedClient;\n  }\n  const newClient = new S3Client({\n    credentials: {\n      accessKeyId: credentials.accessKeyId,\n      secretAccessKey: credentials.secretAccessKey,\n      sessionToken: credentials.sessionToken,\n    },\n    region: credentials.region,\n    useDualstackEndpoint: true,\n  });\n  clientCache.set(cacheKey, newClient);\n  return newClient;\n}\n","/**\n * Converts an S3 URI to a bucket and key\n */\nexport function s3UriToParams(uri: string): { Bucket: string, Key: string } {\n  const matches = /^s3:\\/\\/([^/]+)\\/(.+)$/.exec(uri);\n  if (!matches) {\n    throw new Error(`Received invalid uri: '${uri}'`);\n  }\n  return {\n    Bucket: matches[1],\n    Key: matches[2],\n  };\n}\n\n","import { AWSCredentials } from \"@cirrobio/api-client\";\nimport { GetObjectCommand, GetObjectCommandInput } from \"@aws-sdk/client-s3\";\nimport { getSignedUrl as getSignedUrlInternal } from \"@aws-sdk/s3-request-presigner\";\nimport { createS3Client } from \"../util/s3-client\";\nimport { s3UriToParams } from \"../util/s3-utils\";\n\nexport interface GetFileUrlParams extends GetSignedUrlOptions {\n  url: string;\n  credentials?: AWSCredentials;\n}\n\nexport interface GetSignedUrlOptions {\n  download?: boolean;\n  gzip?: boolean;\n  timeout?: number;\n  filename?: string;\n}\n\n/**\n * Get a signed URL for a file in S3 given its S3 URI.\n * Defaults to a 5 minute timeout.\n */\nexport function getSignedUrl({ url, credentials, ...params }: GetFileUrlParams): Promise<string> {\n  const client = createS3Client(credentials);\n  const { Bucket, Key } = s3UriToParams(url);\n  const fileName = params.filename ?? Key.split('/').pop();\n  const args: GetObjectCommandInput = { Bucket, Key };\n  if (params?.download) {\n    args.ResponseContentDisposition = `attachment; filename=\"${fileName}\"`\n  }\n  if (params?.gzip) {\n    args.ResponseContentEncoding = 'gzip'\n  }\n  const command = new GetObjectCommand(args);\n  return getSignedUrlInternal(client, command, { expiresIn: 60 * (params?.timeout ?? 5) });\n}\n","\nconst resourcePrefix = 'project-';\n\nexport function getResourceName(projectId: string): string {\n  return `${resourcePrefix}${projectId}`;\n}\n\n","import { getResourceName } from \"../util/get-resource-name\";\n\n/**\n * Get the S3 bucket name for a project.\n * Will be deprecated in the future, use domain from manifest instead.\n */\nexport function getProjectS3Bucket(projectId: string): string {\n  return getResourceName(projectId)\n}\n","import { AWSCredentials, GenerateProjectFileAccessTokenRequest, ProjectAccessType } from \"@cirrobio/api-client\";\nimport { ProjectFileAccessContext } from \"./project-access-context\";\nimport { credentialsCache, credentialsMutex } from \"./util/credentials-mutex.so\";\nimport { GetFileUrlParams, getSignedUrl, GetSignedUrlOptions } from \"./actions/sign-url.fn\";\nimport { getProjectS3Bucket } from \"./shared\";\nimport { DownloadableFile } from \"./models/file-object.model\";\n\nexport interface IFileCredentialsApi {\n  generateProjectFileAccessToken: (params: GenerateProjectFileAccessTokenRequest) => Promise<AWSCredentials>;\n}\n\n/**\n * Service for viewing files in Cirro\n *  currently this only operates on files within a project\n */\nexport class FileService {\n  constructor(\n    private readonly fileCredsApi: IFileCredentialsApi\n  ) {}\n\n  /**\n   * Get contents of a file\n   */\n  async getProjectFile(file: DownloadableFile): Promise<Response> {\n    const url = await this.getSignedUrlFromProjectFile(file);\n    return fetch(url);\n  }\n\n  /**\n   * Get a signed URL for a file\n   */\n  async getSignedUrlFromProjectFile(file: DownloadableFile, params?: GetSignedUrlOptions): Promise<string> {\n    const credentials = await this.getProjectAccessCredentials(file.fileAccessContext);\n    const _params: GetFileUrlParams = {\n      ...params,\n      filename: file.name,\n      url: file.url,\n      credentials,\n    };\n    return getSignedUrl(_params);\n  }\n\n  /**\n   * Get a signed URL for a file given a path\n   */\n  async getSignedUrlFromProjectPath(fileAccessContext: ProjectFileAccessContext, path: string, params?: GetSignedUrlOptions): Promise<string> {\n    const credentials = await this.getProjectAccessCredentials(fileAccessContext);\n    const _params: GetFileUrlParams = {\n      ...params,\n      filename: path.split('/').pop(),\n      url: `s3://${getProjectS3Bucket(fileAccessContext.project.id)}/${path}`,\n      credentials,\n    };\n    return getSignedUrl(_params);\n  }\n\n  /**\n   * Get credentials for accessing a project file\n   */\n  async getProjectAccessCredentials(fileAccessContext: ProjectFileAccessContext): Promise<AWSCredentials> {\n    const accessType = fileAccessContext.fileAccessRequest.accessType;\n    // Special case for project download, since we can cache the credentials\n    if (accessType === ProjectAccessType.ProjectDownload || accessType === ProjectAccessType.SharedDatasetDownload) {\n      return this.getProjectReadCredentials(fileAccessContext);\n    }\n    return this.fileCredsApi.generateProjectFileAccessToken({ projectId: fileAccessContext.project.id, projectFileAccessRequest: fileAccessContext.fileAccessRequest });\n  }\n\n  private async getProjectReadCredentials(fileAccessContext: ProjectFileAccessContext): Promise<AWSCredentials> {\n    const projectId = fileAccessContext.project.id;\n    // Append datasetId to cache key for shared dataset downloads since we need to generate a new token for each dataset\n    let cacheKey = projectId;\n    if (fileAccessContext.fileAccessRequest.accessType === ProjectAccessType.SharedDatasetDownload) {\n      cacheKey = `${projectId}-${fileAccessContext.fileAccessRequest.datasetId}`;\n    }\n\n    return credentialsMutex.dispatch(async () => {\n      const cachedCredentials = credentialsCache.get(cacheKey);\n      const expirationTime = cachedCredentials ? cachedCredentials?.expiration : null;\n      const fetchNewCredentials = !expirationTime || expirationTime < new Date();\n      if (fetchNewCredentials) {\n        const projectFileAccessRequest = fileAccessContext.fileAccessRequest;\n        const credentials = await this.fileCredsApi.generateProjectFileAccessToken({ projectId, projectFileAccessRequest });\n        credentialsCache.set(cacheKey, credentials);\n        return credentials;\n      }\n      return cachedCredentials;\n    });\n  }\n}\n","import { AWSCredentials } from \"@cirrobio/api-client\";\nimport { DeleteObjectCommand } from \"@aws-sdk/client-s3\";\nimport { s3UriToParams } from \"../util/s3-utils\";\nimport { createS3Client } from \"../util/s3-client\";\n\nexport interface DeleteFileParams {\n  url: string;\n  credentials: AWSCredentials;\n}\n\n/**\n * Delete a file from S3 given its URL and credentials.\n */\nexport async function deleteFile({ url, credentials }: DeleteFileParams): Promise<void> {\n  const { Bucket, Key } = s3UriToParams(url);\n  const cmd = new DeleteObjectCommand({ Bucket, Key });\n  await createS3Client(credentials).send(cmd);\n}\n","import { Upload } from \"@aws-sdk/lib-storage\";\nimport { AWSCredentials } from '@cirrobio/api-client';\nimport { createS3Client } from \"../util/s3-client\";\nimport { PutObjectCommandInput } from \"@aws-sdk/client-s3\";\n\nexport interface UploadFileParams {\n  bucket: string;\n  path: string;\n  file: File;\n  credentials: AWSCredentials;\n  metadata?: Record<string, string>;\n}\n\n/**\n * Upload a file to S3\n */\nexport function uploadFile({ bucket, path, file, credentials, metadata }: UploadFileParams): Upload {\n  const params: PutObjectCommandInput = {\n    Bucket: bucket,\n    Key: path,\n    Body: file,\n    ContentType: file.type,\n    Metadata: metadata\n  };\n  return new Upload({\n    client: createS3Client(credentials),\n    queueSize: 4,\n    params,\n  });\n}\n\n","import { ProjectAccessType, DatasetDetail, ProjectFileAccessRequest, Project } from \"@cirrobio/api-client\";\n\ntype ProjectIdentifiable = Pick<Project, 'id'>;\n\n/**\n * Helper class to encapsulate the file access for a project.\n */\nexport class ProjectFileAccessContext {\n  constructor(\n    readonly project: ProjectIdentifiable,\n    readonly dataset: DatasetDetail,\n    readonly fileAccessRequest: ProjectFileAccessRequest\n  ) {\n  }\n\n  static projectDownload(project: ProjectIdentifiable): ProjectFileAccessContext {\n    const request: ProjectFileAccessRequest = { accessType: ProjectAccessType.ProjectDownload };\n    return new ProjectFileAccessContext(project, null, request);\n  }\n\n  static datasetDownload(project: ProjectIdentifiable, dataset: DatasetDetail): ProjectFileAccessContext {\n    const accessType = dataset.share ? ProjectAccessType.SharedDatasetDownload : ProjectAccessType.ProjectDownload;\n    const request: ProjectFileAccessRequest = { accessType, datasetId: dataset.id };\n    return new ProjectFileAccessContext(project, dataset, request);\n  }\n}\n","import { ProjectFileAccessContext } from \"../project-access-context\";\n\nexport enum FileSystemObjectType {\n  FILE = 'file',\n  FOLDER = 'folder'\n}\n\n/**\n * Represents a file that can be downloaded\n */\nexport interface DownloadableFile {\n  url: string;\n  name?: string;\n  fileAccessContext: ProjectFileAccessContext;\n}\n\n/**\n * Represents a file in Cirro\n */\nexport interface FileSystemObject extends DownloadableFile {\n  /**\n   * Unique Id For Object\n   */\n  id: string;\n  /**\n   * Object S3 Url\n   */\n  url: string;\n  /**\n   * Object Path\n   */\n  path: string;\n  /**\n   * Object Name\n   */\n  name: string;\n  /**\n   * Object Size\n   */\n  size: number;\n  /**\n   * Object Kind (PNG, TXT)\n   */\n  kind: string;\n  /**\n   * Object Type (File or Folder)\n   */\n  type: FileSystemObjectType;\n  /**\n   * Metadata\n   */\n  metadata?: Record<string, any>;\n  /**\n   * Access context\n   */\n  fileAccessContext: ProjectFileAccessContext;\n}\n","import { FileSystemObject } from \"./models/file-object.model\";\n\n/**\n * Calculate the total size of all files in a directory.\n * @param files - An array of FileSystemObject representing the files in the directory.\n * @return The total size of all files in bytes.\n */\nexport function calculateTotalSize(files: Array<FileSystemObject>): number {\n  let totalSize = 0;\n  for (const file of files) {\n    totalSize += file.size;\n  }\n  return totalSize;\n}\n","/**\n * Pretty prints a JSON object with the specified indentation level.\n * @param obj JSON object to be pretty printed.\n * @param indentLevel Number of spaces to use for indentation.\n */\nexport function jsonPrettyPrint(obj: object, indentLevel=2): string {\n  return JSON.stringify(obj, null, indentLevel);\n}\n","/**\n * Format bytes as human-readable text.\n * @param bytes Number of bytes.\n * @param si True to use metric(SI) units, aka powers of 1000. False to use\n * binary(IEC), aka powers of 1024.\n   * @param dp Number of decimal places to display.\n *\n * @return Formatted string.\n */\nexport function bytesToString(bytes, si = false, dp = 1): string {\n  const thresh = si ? 1000 : 1024;\n\n  if (Math.abs(bytes) < thresh) {\n    return `${bytes} B`;\n  }\n\n  const units = si\n    ? ['kB', 'MB', 'GB', 'TB', 'PB', 'EB', 'ZB', 'YB']\n    : ['KiB', 'MiB', 'GiB', 'TiB', 'PiB', 'EiB', 'ZiB', 'YiB'];\n  let u = -1;\n  const r = 10 ** dp;\n\n  do {\n    bytes /= thresh;\n    ++u;\n  } while (\n    Math.round(Math.abs(bytes) * r) / r >= thresh\n    && u < units.length - 1\n    );\n\n  return `${bytes.toFixed(dp)} ${units[u]}`;\n}\n","/**\n * Normalizes a date to UTC by adjusting for the timezone offset.\n * Useful when you are working with dates that may not include time information.\n * @param date\n */\nexport function normalizeDate(date: Date | string | undefined | null): Date {\n  if (!date) throw new Error(\"Attempt to normalize undefined\");\n  if (!(date instanceof Date)) date = new Date(date);\n  return new Date(date.getTime() - date.getTimezoneOffset() * -60000);\n}\n","/**\n * Normalize a string by trimming it and returning null if it is empty.\n * @param input The string to normalize.\n */\nexport function normalizeString(input: string): string {\n  if (!input?.trim()) return null;\n  return input.trim();\n}\n","/**\n * Removes the starting slash from a path.\n * @param path Input path\n */\nexport function removeStartingSlash(path: string): string {\n  if (!path) return path;\n  if (path.startsWith('./')) return path.substring(2);\n  if (path.startsWith('/')) return path.substring(1);\n  return path;\n}\n\n/**\n * Removes the ending slash from a path.\n * @param path Input path\n */\nexport function removeEndingSlash(path: string): string {\n  return path?.endsWith('/') ? path.slice(0, -1) : path;\n}\n","const dateFormat = new Intl.DateTimeFormat('en-US', { month: '2-digit', day: '2-digit', year: '2-digit' });\n\n/**\n * Converts a date string or Date object to MM/DD/YY date string.\n * Ex., \"2023-10-01\" -> \"10/01/23\"\n * @param date Input date string or Date object.\n */\nexport function toDateFormat(date: string | Date): string {\n  if (!date) return null;\n  const d: Date = (typeof date === 'string') ? new Date(date) : date\n  return dateFormat.format(d);\n}\n","/**\n * Converts a string to Title case.\n * Ex., \"hello world\" -> \"Hello world\"\n * @param value\n */\nexport function toTitleCase(value: string): string {\n  if (!value) return null;\n  return value[0].toUpperCase() + value.slice(1).toLowerCase();\n}\n","import { toTitleCase } from './to-title-case';\n\n/**\n * Converts a field name to a more human-readable format.\n * Ex., \"helloWorld\" -> \"Hello World\"\n * @param value The value to convert.\n */\nexport function toFriendlyName(value: string): string {\n  let _value = value.split(/(?=[A-Z])/).join(' ');\n  _value = _value.split('_').join(' ');\n  _value = _value.split('|').join(' ');\n  _value = _value.replace(/ +/g, ' ');\n  return toTitleCase(_value);\n}\n","const money = new Intl.NumberFormat('en-US', {\n  style: 'currency',\n  currency: 'USD',\n});\n\n/**\n * Converts a number or bigint to a formatted money string.\n * Ex., 1234.56 -> $1,234.56\n * @param value Input number or bigint value.\n */\nexport function toMoney(value: number | bigint): string {\n  return money.format(value as number);\n}\n","/**\n * Converts a string to PascalCase.\n * Ex., \"hello world\" -> \"HelloWorld\"\n * @param value The string to convert.\n */\nexport function toPascalCase(value: string): string {\n  return value.replace(/(\\w)(\\w*)/g, (g0, g1, g2) => g1.toUpperCase() + g2.toLowerCase());\n}\n","import { calculateTotalSize } from \"../calculate-size\";\nimport { bytesToString } from \"../../formatters\";\nimport { FileSystemObject } from \"./file-object.model\";\n\nexport class Assets extends Array<FileSystemObject> {\n  private _totalSize: string;\n  private _totalSizeBytes: number;\n\n  // Total size of all files in human-readable format\n  get totalSize(): string {\n    if (!this._totalSize) {\n      this.calculateSize();\n    }\n    return this._totalSize;\n  }\n\n  get totalSizeBytes(): number {\n    if (!this._totalSizeBytes) {\n      this.calculateSize();\n    }\n    return this._totalSizeBytes;\n  }\n  private calculateSize(): void {\n    this._totalSizeBytes = calculateTotalSize(this);\n    this._totalSize = bytesToString(this._totalSizeBytes)\n  }\n}\n","import { v4 as uuidv4 } from 'uuid';\nimport { FileSystemObject, FileSystemObjectType } from \"./file-object.model\";\n\nexport class Folder implements FileSystemObject {\n  readonly id: string;\n  readonly url: string;\n  readonly path: string;\n  readonly name: string;\n  readonly domain: string;\n  readonly kind = 'Folder';\n  readonly fileAccessContext = null;\n  readonly size = 0;\n  readonly type = FileSystemObjectType.FOLDER;\n\n  constructor(url: string, name: string, path: string, domain: string) {\n    this.id = uuidv4();\n    this.url = url;\n    this.name = name;\n    this.path = path;\n    this.domain = domain;\n  }\n}\n","import { FileSystemObject, FileSystemObjectType } from \"./file-object.model\";\nimport { ProjectFileAccessContext } from \"../project-access-context\";\nimport { v4 as uuidv4 } from 'uuid';\n\nexport class File implements FileSystemObject {\n  readonly id: string;\n  readonly url: string\n  readonly size: number;\n  readonly path: string;\n  readonly name: string;\n  readonly metadata: Record<string, any>;\n  readonly fileAccessContext: ProjectFileAccessContext;\n\n  get type() {\n    return FileSystemObjectType.FILE;\n  }\n\n  get kind() {\n    return this.path.slice(this.\n    path.lastIndexOf('.') + 1);\n  }\n\n  constructor(domain: string, file: string, size: number, metadata: Record<string, any>, accessContext: ProjectFileAccessContext) {\n    this.id = uuidv4();\n    this.url = `${domain}/${file}`;\n    this.size = size;\n    this.metadata = metadata;\n    this.fileAccessContext = accessContext;\n\n    const fileFolderIdx = file.lastIndexOf('/');\n    if (fileFolderIdx === -1) {\n      this.path = '';\n      this.name = file;\n    } else {\n      this.path = file.substring(0, fileFolderIdx);\n      this.name = file.substring(fileFolderIdx + 1);\n    }\n  }\n}\n","import { DatasetAssetsManifest, FileEntry } from '@cirrobio/api-client';\nimport { Assets } from \"./models/assets\";\nimport { Folder } from \"./models/folder\";\nimport { File } from \"./models/file\";\nimport { ProjectFileAccessContext } from \"./project-access-context\";\nimport { removeEndingSlash } from \"../formatters\";\n\n\nexport class ManifestParser {\n  private readonly manifest: DatasetAssetsManifest;\n  private readonly accessContext: ProjectFileAccessContext;\n\n  constructor(manifest: DatasetAssetsManifest, accessContext?: ProjectFileAccessContext) {\n    this.manifest = manifest;\n    this.accessContext = accessContext;\n  }\n\n  private get files(): Array<FileEntry> {\n    return this.manifest?.files ?? [];\n  }\n\n  /**\n   * Generates asset objects from the manifest, optionally including folder entries.\n   */\n  public generateAssets(generateFolders = false): Assets {\n    const domain = removeEndingSlash(this.manifest?.domain);\n    const assets = new Assets();\n\n    for (const file of this.files) {\n      assets.push(new File(domain, file.path, file.size, file.metadata, this.accessContext));\n    }\n\n    // Optionally add folder entries\n    if (generateFolders) {\n      assets.push(...this.generateFolderAssets(assets, domain));\n    }\n\n    return assets;\n  }\n\n  // Create folder entries, useful for visualizing folders as items in a file browser\n  private generateFolderAssets(assets: Assets, domain: string): Folder[] {\n    const folderSet = new Set<string>();\n\n    // Collect all unique folder paths\n    for (const asset of assets) {\n      const parts = asset.path.split('/').filter(p => p.length > 0);\n      let currentPath = '';\n      for (const part of parts) {\n        currentPath = currentPath ? `${currentPath}/${part}` : part;\n        folderSet.add(currentPath);\n      }\n    }\n\n    // Create Folder objects from unique paths\n    return Array.from(folderSet)\n      .map(folderPath => {\n        const name = folderPath.substring(folderPath.lastIndexOf('/') + 1);\n        const parentPath = folderPath.includes('/') ? folderPath.substring(0, folderPath.lastIndexOf('/')) : '';\n        return new Folder(folderPath, name, parentPath, domain);\n      });\n  }\n}\n","\n/**\n * Returns the parent directory of a given file path.\n */\nexport function getParentPath(path: string): string {\n  return path.split(\"/\").slice(0, -1).join(\"/\") ?? \"\"\n}\n","export class ApiError extends Error {\n  errors: string[];\n\n  constructor(message: string, errors: string[]) {\n    super(message);\n    this.errors = errors;\n  }\n}\n","import { Middleware, ResponseContext } from \"@cirrobio/api-client\";\nimport { ApiError } from \"./error\";\n\nexport class PortalErrorHandler implements Middleware {\n  async post(context: ResponseContext): Promise<Response | void> {\n    const { response } = context;\n    if (response && (response.status >= 200 && response.status < 300)) {\n      return response;\n    }\n\n    // Handle Error\n    let errorMessage: string;\n    const errors = [];\n    try {\n      const err = await response.json();\n      console.warn(err);\n      if ('errorDetail' in err) {\n        errorMessage = err.errorDetail;\n        errors.push(err.errors.map((e: any) => e.message));\n      } else {\n        errorMessage = err.message;\n      }\n    } catch (ignore) {\n      errorMessage = \"Unknown Error\";\n    }\n    throw new ApiError(errorMessage, errors);\n  }\n}\n","import { PortalErrorHandler } from \"./error-handler\";\nimport { Configuration } from \"@cirrobio/api-client\";\n\ninterface GetConfigParams {\n  tokenGetter: () => Promise<string>;\n  basePath?: string;\n}\n\nexport const generateApiConfig = ({ basePath = \"/api\", tokenGetter}: GetConfigParams) => {\n  return new Configuration({\n    basePath,\n    accessToken: tokenGetter,\n    middleware: [\n      new PortalErrorHandler()\n    ],\n  });\n}\n","export class CurrentUser {\n  username: string;\n  /**\n   * The unique identifier for the user\n   */\n  sub: string\n\n  /**\n   * The time the user authenticated\n   */\n  authTime: Date;\n\n  /**\n   * The groups the user belongs to\n   */\n  groups: string[];\n\n  static fromCognitoUser(idTokenPayload: Record<string, any>): CurrentUser {\n    return {\n      username: idTokenPayload[\"cognito:username\"] ?? idTokenPayload.username,\n      sub: idTokenPayload.sub,\n      authTime: new Date(idTokenPayload.auth_time * 1000),\n      groups: idTokenPayload[\"cognito:groups\"] ?? [],\n    };\n  }\n}\n","import { SystemInfoResponse } from \"@cirrobio/api-client\";\nimport { AuthenticationProvider } from \"./authentication-provider\";\nimport { CurrentUser } from \"./current-user\";\n\n\nexport class StaticTokenAuthProvider implements AuthenticationProvider {\n  constructor(\n    readonly token: string\n  ) {\n  }\n\n  public configure(_ignore: SystemInfoResponse): void {\n    console.log('StaticTokenAuthProvider loaded');\n  }\n\n  public async getAccessToken() {\n    return this.token;\n  }\n\n  public async getCurrentUser() {\n    const accessToken = await this.getAccessToken();\n    const parsedToken = JSON.parse(atob(accessToken.split('.')[1]));\n    return CurrentUser.fromCognitoUser(parsedToken);\n  }\n\n  public forceRefresh(): Promise<void> {\n    return Promise.resolve();\n  }\n}\n","import {\n  AuditApi,\n  BillingApi,\n  ComputeEnvironmentApi,\n  Configuration,\n  DatasetsApi,\n  ExecutionApi,\n  FileApi,\n  GovernanceApi,\n  MetadataApi,\n  NotebooksApi,\n  ProcessesApi,\n  ProjectRequestsApi,\n  ProjectsApi,\n  ReferencesApi,\n  SharingApi,\n  SystemApi,\n  ToolsApi,\n  UsersApi\n} from \"@cirrobio/api-client\";\nimport { generateApiConfig } from \"../api/config\";\n\ninterface DataServiceParams {\n  tokenGetter: () => Promise<string>;\n  basePath?: string;\n}\n\nexport class DataService {\n  private readonly apiConfig: Configuration;\n\n  private readonly _auditApi: AuditApi;\n  private readonly _billingApi: BillingApi;\n  private readonly _computeEnvironmentApi: ComputeEnvironmentApi;\n  private readonly _datasetsApi: DatasetsApi;\n  private readonly _executionApi: ExecutionApi;\n  private readonly _fileApi: FileApi;\n  private readonly _governanceApi: GovernanceApi;\n  private readonly _metadataApi: MetadataApi;\n  private readonly _notebooksApi: NotebooksApi;\n  private readonly _processesApi: ProcessesApi;\n  private readonly _projectRequestsApi: ProjectRequestsApi;\n  private readonly _projectsApi: ProjectsApi;\n  private readonly _referencesApi: ReferencesApi;\n  private readonly _sharingApi: SharingApi;\n  private readonly _systemApi: SystemApi;\n  private readonly _toolsApi: ToolsApi;\n  private readonly _usersApi: UsersApi;\n\n  constructor({ tokenGetter, basePath = \"/api\" }: DataServiceParams) {\n    this.apiConfig = generateApiConfig({ basePath, tokenGetter });\n\n    this._auditApi = new AuditApi(this.apiConfig);\n    this._billingApi = new BillingApi(this.apiConfig);\n    this._computeEnvironmentApi = new ComputeEnvironmentApi(this.apiConfig);\n    this._datasetsApi = new DatasetsApi(this.apiConfig);\n    this._executionApi = new ExecutionApi(this.apiConfig);\n    this._fileApi = new FileApi(this.apiConfig);\n    this._governanceApi = new GovernanceApi(this.apiConfig);\n    this._metadataApi = new MetadataApi(this.apiConfig);\n    this._notebooksApi = new NotebooksApi(this.apiConfig);\n    this._processesApi = new ProcessesApi(this.apiConfig);\n    this._projectRequestsApi = new ProjectRequestsApi(this.apiConfig);\n    this._projectsApi = new ProjectsApi(this.apiConfig);\n    this._referencesApi = new ReferencesApi(this.apiConfig);\n    this._sharingApi = new SharingApi(this.apiConfig);\n    this._systemApi = new SystemApi(this.apiConfig);\n    this._toolsApi = new ToolsApi(this.apiConfig);\n    this._usersApi = new UsersApi(this.apiConfig);\n  }\n\n  get audit(): AuditApi {\n    return this._auditApi;\n  }\n  get billing(): BillingApi {\n    return this._billingApi;\n  }\n  get computeEnvironments(): ComputeEnvironmentApi {\n    return this._computeEnvironmentApi;\n  }\n  get datasets(): DatasetsApi {\n    return this._datasetsApi;\n  }\n  get execution(): ExecutionApi {\n    return this._executionApi;\n  }\n  get file(): FileApi {\n    return this._fileApi;\n  }\n  get governance(): GovernanceApi {\n    return this._governanceApi;\n  }\n  get metadata(): MetadataApi {\n    return this._metadataApi;\n  }\n  get notebooks(): NotebooksApi {\n    return this._notebooksApi;\n  }\n  get processes(): ProcessesApi {\n    return this._processesApi;\n  }\n  get projectRequests(): ProjectRequestsApi {\n    return this._projectRequestsApi;\n  }\n  get projects(): ProjectsApi {\n    return this._projectsApi;\n  }\n  get references(): ReferencesApi {\n    return this._referencesApi;\n  }\n  get sharing(): SharingApi {\n    return this._sharingApi;\n  }\n  get system(): SystemApi {\n    return this._systemApi;\n  }\n  get tools(): ToolsApi {\n    return this._toolsApi;\n  }\n  get users(): UsersApi {\n    return this._usersApi;\n  }\n}\n","/**\n * Extracts a value from an object using the json path notation, i.e. $.test.id\n * @param path JSON path to the value\n * @param obj Object to extract the value from\n */\nexport function extractFromObject(path: string, obj: object): any {\n  const pathParts = path.slice(2).split('.')\n  return pathParts.reduce(function(o, k) {\n    return o && o[k];\n  }, obj);\n}\n","/**\n * Ignores dangling promise 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 // TODO: put back bam\nexport const FILE_TRACK_VARIANT = ['vcf', 'vcf.gz'];\nexport const FILE_TRACK_WIG = ['wig', 'wig.gz', 'bw', 'bw.gz', 'bigwig', 'bigwig.gz'];\nexport const FILE_TRACK_SEG = ['seg', 'seg.gz'];\nexport const FILE_TRACK_INDEX_EXTENSIONS = ['tbi', 'bai', 'crai', 'csi'];\nexport const FILE_VITESSCE_EXTENSIONS = ['hdf5', 'h5ad', 'loom'];\nexport const FILE_TRACK_EXTENSIONS_NO_INDEX = [\n    ...FILE_TRACK_ANNOTATION,\n    ...FILE_TRACK_ALIGNMENTS,\n    ...FILE_TRACK_VARIANT,\n    ...FILE_TRACK_WIG,\n    ...FILE_TRACK_SEG\n];\nexport const FILE_TRACK_EXTENSIONS = [\n    ...FILE_TRACK_EXTENSIONS_NO_INDEX,\n    ...FILE_TRACK_INDEX_EXTENSIONS\n]\n\n\nexport const FILE_BROWSER_EXTENSIONS = ['html', 'pdf'];\n\n\n/**\n * An array of file extensions that are protein structure files.\n */\nexport const FILE_PROTEIN_STRUCTURE_EXTENSIONS = ['pdb', 'pdb.gz', 'cif', 'cif.gz', 'ent', 'ent.gz', 'mmtf', 'mmtf.gz'];\n/**\n * An array of file extensions that are considered tabular files.\n */\nexport const FILE_DSV_EXTENSIONS = ['tab', 'csv', 'tsv', 'dsv'];\n/**\n * An array of file extensions that contain genomic sequence content.\n */\nexport const FILE_TXT_GENOMICS_EXTENSIONS = ['fasta', 'fna', 'fsa', 'fa', 'fastp', 'fastq', 'faa', 'gbk', 'gff', 'vcf', 'seq'];\n\n/**\n * An array of file extensions that are considered TXT files.\n */\nexport const FILE_TXT_EXTENSIONS = ['txt', 'log', 'yml', 'cfg', 'config', 'xml', 'yaml', ...FILE_DSV_EXTENSIONS, ...FILE_TXT_GENOMICS_EXTENSIONS];\n\n\n/**\n * An array of file extensions that are considered image files.\n */\nexport const FILE_IMAGE_EXTENSIONS = ['jpg', 'jpeg', 'png', 'svg'];\n\n/**\n * An array of file extensions that are considered OME (Open Microscopy Environment) files.\n */\nexport const FILE_OME_EXTENSIONS = ['tif', 'ome.tif', 'ome.tiff', 'ome.tif.gz', 'ome.tiff.gz'];\n\n/**\n * An array of file extensions that can be opened in the browser.\n * Includes common document formats such as HTML, PDF, and JSON, as well as image, DSV, TXT, and OME file formats.\n */\nexport const FILE_EXTENSIONS_TO_OPEN = ['html', 'pdf', 'json', 'fcs',\n    ...FILE_IMAGE_EXTENSIONS,\n    ...FILE_TXT_EXTENSIONS,\n    ...FILE_TRACK_EXTENSIONS,\n    ...FILE_PROTEIN_STRUCTURE_EXTENSIONS\n];\n\n\n/**\n * Checks if a file has an extension that matches one in the provided list.\n * @param filePath The file to check the extension of.\n * @param extensions A list of file endings to check the file against.\n * @returns True or false if the file has an ending in the extensions list.\n */\nexport function matchesExtension(filePath: string, extensions: string[]): boolean {\n    filePath = filePath.toLowerCase();\n\n    // Decompress the filePath if it ends with .gz\n    if (filePath.endsWith('.gz')) {\n        filePath = filePath.slice(0, -3);  // remove the .gz extension\n    }\n\n    // Now, get the extension of the file\n    const fileExtension = filePath.slice(filePath.lastIndexOf('.') + 1);\n\n    // Check if the fileExtension is in the list of extensions\n    return extensions.includes(fileExtension);\n}\n","import { AWSCredentials } from '@cirrobio/api-client';\n\nclass Mutex<T> {\n  private mutex = Promise.resolve();\n\n  lock(): PromiseLike<() => void> {\n    let begin: (unlock: () => void) => void = () => { /* Do nothing */ };\n\n    this.mutex = this.mutex.then(() => new Promise(begin));\n\n    return new Promise((res) => {\n      begin = res;\n    });\n  }\n\n  async dispatch(fn: (() => T) | (() => PromiseLike<T>)): Promise<T> {\n    const unlock = await this.lock();\n    try {\n      return await Promise.resolve(fn());\n    } finally {\n      unlock();\n    }\n  }\n}\n\n/**\n * A mutex to ensure that only one request for credentials is made at a time.\n */\nexport const credentialsMutex = new Mutex<AWSCredentials>();\n/**\n * A cache of credentials to avoid making multiple requests for the same credentials.\n */\nexport const credentialsCache: Map<string, AWSCredentials> = new Map<string, AWSCredentials>();\n","import { S3Client } from \"@aws-sdk/client-s3\";\nimport { AWSCredentials } from \"@cirrobio/api-client\";\n\nconst clientCache = new Map<string, S3Client>();\n\n/**\n * Creates an S3 client using the provided credentials.\n */\nexport function createS3Client(credentials: AWSCredentials): S3Client {\n  const cacheKey = `${credentials.accessKeyId}-${credentials.region}`;\n  const cachedClient = clientCache.get(cacheKey);\n  if (cachedClient) {\n    return cachedClient;\n  }\n  const newClient = new S3Client({\n    credentials: {\n      accessKeyId: credentials.accessKeyId,\n      secretAccessKey: credentials.secretAccessKey,\n      sessionToken: credentials.sessionToken,\n    },\n    region: credentials.region,\n    useDualstackEndpoint: true,\n  });\n  clientCache.set(cacheKey, newClient);\n  return newClient;\n}\n","/**\n * Converts an S3 URI to a bucket and key\n */\nexport function s3UriToParams(uri: string): { Bucket: string, Key: string } {\n  const matches = /^s3:\\/\\/([^/]+)\\/(.+)$/.exec(uri);\n  if (!matches) {\n    throw new Error(`Received invalid uri: '${uri}'`);\n  }\n  return {\n    Bucket: matches[1],\n    Key: matches[2],\n  };\n}\n\n","import { AWSCredentials } from \"@cirrobio/api-client\";\nimport { GetObjectCommand, GetObjectCommandInput } from \"@aws-sdk/client-s3\";\nimport { getSignedUrl as getSignedUrlInternal } from \"@aws-sdk/s3-request-presigner\";\nimport { createS3Client } from \"../util/s3-client\";\nimport { s3UriToParams } from \"../util/s3-utils\";\n\nexport interface GetFileUrlParams extends GetSignedUrlOptions {\n  url: string;\n  credentials?: AWSCredentials;\n}\n\nexport interface GetSignedUrlOptions {\n  download?: boolean;\n  gzip?: boolean;\n  timeout?: number;\n  filename?: string;\n}\n\n/**\n * Get a signed URL for a file in S3 given its S3 URI.\n * Defaults to a 5 minute timeout.\n */\nexport function getSignedUrl({ url, credentials, ...params }: GetFileUrlParams): Promise<string> {\n  const client = createS3Client(credentials);\n  const { Bucket, Key } = s3UriToParams(url);\n  const fileName = params.filename ?? Key.split('/').pop();\n  const args: GetObjectCommandInput = { Bucket, Key };\n  if (params?.download) {\n    args.ResponseContentDisposition = `attachment; filename=\"${fileName}\"`\n  }\n  if (params?.gzip) {\n    args.ResponseContentEncoding = 'gzip'\n  }\n  const command = new GetObjectCommand(args);\n  return getSignedUrlInternal(client, command, { expiresIn: 60 * (params?.timeout ?? 5) });\n}\n","\nconst resourcePrefix = 'project-';\n\nexport function getResourceName(projectId: string): string {\n  return `${resourcePrefix}${projectId}`;\n}\n\n","import { getResourceName } from \"../util/get-resource-name\";\n\n/**\n * Get the S3 bucket name for a project.\n * Will be deprecated in the future, use domain from manifest instead.\n */\nexport function getProjectS3Bucket(projectId: string): string {\n  return getResourceName(projectId)\n}\n","import { AWSCredentials, GenerateProjectFileAccessTokenRequest, ProjectAccessType } from \"@cirrobio/api-client\";\nimport { ProjectFileAccessContext } from \"./project-access-context\";\nimport { credentialsCache, credentialsMutex } from \"./util/credentials-mutex.so\";\nimport { GetFileUrlParams, getSignedUrl, GetSignedUrlOptions } from \"./actions/sign-url.fn\";\nimport { getProjectS3Bucket } from \"./shared\";\nimport { DownloadableFile } from \"./models/file-object.model\";\n\nexport interface IFileCredentialsApi {\n  generateProjectFileAccessToken: (params: GenerateProjectFileAccessTokenRequest) => Promise<AWSCredentials>;\n}\n\n/**\n * Service for viewing files in Cirro\n *  currently this only operates on files within a project\n */\nexport class FileService {\n  constructor(\n    private readonly fileCredsApi: IFileCredentialsApi\n  ) {}\n\n  /**\n   * Get contents of a file\n   */\n  async getProjectFile(file: DownloadableFile): Promise<Response> {\n    const url = await this.getSignedUrlFromProjectFile(file);\n    return fetch(url);\n  }\n\n  /**\n   * Get a signed URL for a file\n   */\n  async getSignedUrlFromProjectFile(file: DownloadableFile, params?: GetSignedUrlOptions): Promise<string> {\n    const credentials = await this.getProjectAccessCredentials(file.fileAccessContext);\n    const _params: GetFileUrlParams = {\n      ...params,\n      filename: file.name,\n      url: file.url,\n      credentials,\n    };\n    return getSignedUrl(_params);\n  }\n\n  /**\n   * Get a signed URL for a file given a path\n   */\n  async getSignedUrlFromProjectPath(fileAccessContext: ProjectFileAccessContext, path: string, params?: GetSignedUrlOptions): Promise<string> {\n    const credentials = await this.getProjectAccessCredentials(fileAccessContext);\n    const _params: GetFileUrlParams = {\n      ...params,\n      filename: path.split('/').pop(),\n      url: `s3://${getProjectS3Bucket(fileAccessContext.project.id)}/${path}`,\n      credentials,\n    };\n    return getSignedUrl(_params);\n  }\n\n  /**\n   * Get credentials for accessing a project file\n   */\n  async getProjectAccessCredentials(fileAccessContext: ProjectFileAccessContext): Promise<AWSCredentials> {\n    const accessType = fileAccessContext.fileAccessRequest.accessType;\n    // Special case for project download, since we can cache the credentials\n    if (accessType === ProjectAccessType.ProjectDownload || accessType === ProjectAccessType.SharedDatasetDownload) {\n      return this.getProjectReadCredentials(fileAccessContext);\n    }\n    return this.fileCredsApi.generateProjectFileAccessToken({ projectId: fileAccessContext.project.id, projectFileAccessRequest: fileAccessContext.fileAccessRequest });\n  }\n\n  private async getProjectReadCredentials(fileAccessContext: ProjectFileAccessContext): Promise<AWSCredentials> {\n    const projectId = fileAccessContext.project.id;\n    // Append datasetId to cache key for shared dataset downloads since we need to generate a new token for each dataset\n    let cacheKey = projectId;\n    if (fileAccessContext.fileAccessRequest.accessType === ProjectAccessType.SharedDatasetDownload) {\n      cacheKey = `${projectId}-${fileAccessContext.fileAccessRequest.datasetId}`;\n    }\n\n    return credentialsMutex.dispatch(async () => {\n      const cachedCredentials = credentialsCache.get(cacheKey);\n      const expirationTime = cachedCredentials ? cachedCredentials?.expiration : null;\n      const fetchNewCredentials = !expirationTime || expirationTime < new Date();\n      if (fetchNewCredentials) {\n        const projectFileAccessRequest = fileAccessContext.fileAccessRequest;\n        const credentials = await this.fileCredsApi.generateProjectFileAccessToken({ projectId, projectFileAccessRequest });\n        credentialsCache.set(cacheKey, credentials);\n        return credentials;\n      }\n      return cachedCredentials;\n    });\n  }\n}\n","import { AWSCredentials } from \"@cirrobio/api-client\";\nimport { DeleteObjectCommand } from \"@aws-sdk/client-s3\";\nimport { s3UriToParams } from \"../util/s3-utils\";\nimport { createS3Client } from \"../util/s3-client\";\n\nexport interface DeleteFileParams {\n  url: string;\n  credentials: AWSCredentials;\n}\n\n/**\n * Delete a file from S3 given its URL and credentials.\n */\nexport async function deleteFile({ url, credentials }: DeleteFileParams): Promise<void> {\n  const { Bucket, Key } = s3UriToParams(url);\n  const cmd = new DeleteObjectCommand({ Bucket, Key });\n  await createS3Client(credentials).send(cmd);\n}\n","import { Upload } from \"@aws-sdk/lib-storage\";\nimport { AWSCredentials } from '@cirrobio/api-client';\nimport { createS3Client } from \"../util/s3-client\";\nimport { PutObjectCommandInput } from \"@aws-sdk/client-s3\";\nimport { CreateMultipartUploadRequest } from \"@aws-sdk/client-s3/dist-types/models/models_0\";\n\nexport interface UploadFileParams {\n  bucket: string;\n  path: string;\n  file: File;\n  credentials: AWSCredentials;\n  metadata?: Record<string, string>;\n}\n\n/**\n * Upload a file to S3\n */\nexport function uploadFile({ bucket, path, file, credentials, metadata }: UploadFileParams): Upload {\n  const params: PutObjectCommandInput & CreateMultipartUploadRequest = {\n    Bucket: bucket,\n    Key: path,\n    Body: file,\n    ContentType: file.type,\n    Metadata: metadata,\n    ChecksumType: \"FULL_OBJECT\"\n  };\n  return new Upload({\n    client: createS3Client(credentials),\n    queueSize: 4,\n    params,\n  });\n}\n\n","import { ProjectAccessType, DatasetDetail, ProjectFileAccessRequest, Project } from \"@cirrobio/api-client\";\n\ntype ProjectIdentifiable = Pick<Project, 'id'>;\n\n/**\n * Helper class to encapsulate the file access for a project.\n */\nexport class ProjectFileAccessContext {\n  constructor(\n    readonly project: ProjectIdentifiable,\n    readonly dataset: DatasetDetail,\n    readonly fileAccessRequest: ProjectFileAccessRequest\n  ) {\n  }\n\n  static projectDownload(project: ProjectIdentifiable): ProjectFileAccessContext {\n    const request: ProjectFileAccessRequest = { accessType: ProjectAccessType.ProjectDownload };\n    return new ProjectFileAccessContext(project, null, request);\n  }\n\n  static datasetDownload(project: ProjectIdentifiable, dataset: DatasetDetail): ProjectFileAccessContext {\n    const accessType = dataset.share ? ProjectAccessType.SharedDatasetDownload : ProjectAccessType.ProjectDownload;\n    const request: ProjectFileAccessRequest = { accessType, datasetId: dataset.id };\n    return new ProjectFileAccessContext(project, dataset, request);\n  }\n}\n","import { ProjectFileAccessContext } from \"../project-access-context\";\n\nexport enum FileSystemObjectType {\n  FILE = 'file',\n  FOLDER = 'folder'\n}\n\n/**\n * Represents a file that can be downloaded\n */\nexport interface DownloadableFile {\n  url: string;\n  name?: string;\n  fileAccessContext: ProjectFileAccessContext;\n}\n\n/**\n * Represents a file in Cirro\n */\nexport interface FileSystemObject extends DownloadableFile {\n  /**\n   * Unique Id For Object\n   */\n  id: string;\n  /**\n   * Object S3 Url\n   */\n  url: string;\n  /**\n   * Object Path\n   */\n  path: string;\n  /**\n   * Object Name\n   */\n  name: string;\n  /**\n   * Object Size\n   */\n  size: number;\n  /**\n   * Object Kind (PNG, TXT)\n   */\n  kind: string;\n  /**\n   * Object Type (File or Folder)\n   */\n  type: FileSystemObjectType;\n  /**\n   * Metadata\n   */\n  metadata?: Record<string, any>;\n  /**\n   * Access context\n   */\n  fileAccessContext: ProjectFileAccessContext;\n}\n","import { FileSystemObject } from \"./models/file-object.model\";\n\n/**\n * Calculate the total size of all files in a directory.\n * @param files - An array of FileSystemObject representing the files in the directory.\n * @return The total size of all files in bytes.\n */\nexport function calculateTotalSize(files: Array<FileSystemObject>): number {\n  let totalSize = 0;\n  for (const file of files) {\n    totalSize += file.size;\n  }\n  return totalSize;\n}\n","/**\n * Pretty prints a JSON object with the specified indentation level.\n * @param obj JSON object to be pretty printed.\n * @param indentLevel Number of spaces to use for indentation.\n */\nexport function jsonPrettyPrint(obj: object, indentLevel=2): string {\n  return JSON.stringify(obj, null, indentLevel);\n}\n","/**\n * Format bytes as human-readable text.\n * @param bytes Number of bytes.\n * @param si True to use metric(SI) units, aka powers of 1000. False to use\n * binary(IEC), aka powers of 1024.\n   * @param dp Number of decimal places to display.\n *\n * @return Formatted string.\n */\nexport function bytesToString(bytes, si = false, dp = 1): string {\n  const thresh = si ? 1000 : 1024;\n\n  if (Math.abs(bytes) < thresh) {\n    return `${bytes} B`;\n  }\n\n  const units = si\n    ? ['kB', 'MB', 'GB', 'TB', 'PB', 'EB', 'ZB', 'YB']\n    : ['KiB', 'MiB', 'GiB', 'TiB', 'PiB', 'EiB', 'ZiB', 'YiB'];\n  let u = -1;\n  const r = 10 ** dp;\n\n  do {\n    bytes /= thresh;\n    ++u;\n  } while (\n    Math.round(Math.abs(bytes) * r) / r >= thresh\n    && u < units.length - 1\n    );\n\n  return `${bytes.toFixed(dp)} ${units[u]}`;\n}\n","/**\n * Normalizes a date to UTC by adjusting for the timezone offset.\n * Useful when you are working with dates that may not include time information.\n * @param date\n */\nexport function normalizeDate(date: Date | string | undefined | null): Date {\n  if (!date) throw new Error(\"Attempt to normalize undefined\");\n  if (!(date instanceof Date)) date = new Date(date);\n  return new Date(date.getTime() - date.getTimezoneOffset() * -60000);\n}\n","/**\n * Normalize a string by trimming it and returning null if it is empty.\n * @param input The string to normalize.\n */\nexport function normalizeString(input: string): string {\n  if (!input?.trim()) return null;\n  return input.trim();\n}\n","/**\n * Removes the starting slash from a path.\n * @param path Input path\n */\nexport function removeStartingSlash(path: string): string {\n  if (!path) return path;\n  if (path.startsWith('./')) return path.substring(2);\n  if (path.startsWith('/')) return path.substring(1);\n  return path;\n}\n\n/**\n * Removes the ending slash from a path.\n * @param path Input path\n */\nexport function removeEndingSlash(path: string): string {\n  return path?.endsWith('/') ? path.slice(0, -1) : path;\n}\n","const dateFormat = new Intl.DateTimeFormat('en-US', { month: '2-digit', day: '2-digit', year: '2-digit' });\n\n/**\n * Converts a date string or Date object to MM/DD/YY date string.\n * Ex., \"2023-10-01\" -> \"10/01/23\"\n * @param date Input date string or Date object.\n */\nexport function toDateFormat(date: string | Date): string {\n  if (!date) return null;\n  const d: Date = (typeof date === 'string') ? new Date(date) : date\n  return dateFormat.format(d);\n}\n","/**\n * Converts a string to Title case.\n * Ex., \"hello world\" -> \"Hello world\"\n * @param value\n */\nexport function toTitleCase(value: string): string {\n  if (!value) return null;\n  return value[0].toUpperCase() + value.slice(1).toLowerCase();\n}\n","import { toTitleCase } from './to-title-case';\n\n/**\n * Converts a field name to a more human-readable format.\n * Ex., \"helloWorld\" -> \"Hello World\"\n * @param value The value to convert.\n */\nexport function toFriendlyName(value: string): string {\n  let _value = value.split(/(?=[A-Z])/).join(' ');\n  _value = _value.split('_').join(' ');\n  _value = _value.split('|').join(' ');\n  _value = _value.replace(/ +/g, ' ');\n  return toTitleCase(_value);\n}\n","const money = new Intl.NumberFormat('en-US', {\n  style: 'currency',\n  currency: 'USD',\n});\n\n/**\n * Converts a number or bigint to a formatted money string.\n * Ex., 1234.56 -> $1,234.56\n * @param value Input number or bigint value.\n */\nexport function toMoney(value: number | bigint): string {\n  return money.format(value as number);\n}\n","/**\n * Converts a string to PascalCase.\n * Ex., \"hello world\" -> \"HelloWorld\"\n * @param value The string to convert.\n */\nexport function toPascalCase(value: string): string {\n  return value.replace(/(\\w)(\\w*)/g, (g0, g1, g2) => g1.toUpperCase() + g2.toLowerCase());\n}\n","import { calculateTotalSize } from \"../calculate-size\";\nimport { bytesToString } from \"../../formatters\";\nimport { FileSystemObject } from \"./file-object.model\";\n\nexport class Assets extends Array<FileSystemObject> {\n  private _totalSize: string;\n  private _totalSizeBytes: number;\n\n  // Total size of all files in human-readable format\n  get totalSize(): string {\n    if (!this._totalSize) {\n      this.calculateSize();\n    }\n    return this._totalSize;\n  }\n\n  get totalSizeBytes(): number {\n    if (!this._totalSizeBytes) {\n      this.calculateSize();\n    }\n    return this._totalSizeBytes;\n  }\n  private calculateSize(): void {\n    this._totalSizeBytes = calculateTotalSize(this);\n    this._totalSize = bytesToString(this._totalSizeBytes)\n  }\n}\n","import { v4 as uuidv4 } from 'uuid';\nimport { FileSystemObject, FileSystemObjectType } from \"./file-object.model\";\n\nexport class Folder implements FileSystemObject {\n  readonly id: string;\n  readonly url: string;\n  readonly path: string;\n  readonly name: string;\n  readonly domain: string;\n  readonly kind = 'Folder';\n  readonly fileAccessContext = null;\n  readonly size = 0;\n  readonly type = FileSystemObjectType.FOLDER;\n\n  constructor(url: string, name: string, path: string, domain: string) {\n    this.id = uuidv4();\n    this.url = url;\n    this.name = name;\n    this.path = path;\n    this.domain = domain;\n  }\n}\n","import { FileSystemObject, FileSystemObjectType } from \"./file-object.model\";\nimport { ProjectFileAccessContext } from \"../project-access-context\";\nimport { v4 as uuidv4 } from 'uuid';\n\nexport class File implements FileSystemObject {\n  readonly id: string;\n  readonly url: string\n  readonly size: number;\n  readonly path: string;\n  readonly name: string;\n  readonly metadata: Record<string, any>;\n  readonly fileAccessContext: ProjectFileAccessContext;\n\n  get type() {\n    return FileSystemObjectType.FILE;\n  }\n\n  get kind() {\n    return this.path.slice(this.\n    path.lastIndexOf('.') + 1);\n  }\n\n  constructor(domain: string, file: string, size: number, metadata: Record<string, any>, accessContext: ProjectFileAccessContext) {\n    this.id = uuidv4();\n    this.url = `${domain}/${file}`;\n    this.size = size;\n    this.metadata = metadata;\n    this.fileAccessContext = accessContext;\n\n    const fileFolderIdx = file.lastIndexOf('/');\n    if (fileFolderIdx === -1) {\n      this.path = '';\n      this.name = file;\n    } else {\n      this.path = file.substring(0, fileFolderIdx);\n      this.name = file.substring(fileFolderIdx + 1);\n    }\n  }\n}\n","import { DatasetAssetsManifest, FileEntry } from '@cirrobio/api-client';\nimport { Assets } from \"./models/assets\";\nimport { Folder } from \"./models/folder\";\nimport { File } from \"./models/file\";\nimport { ProjectFileAccessContext } from \"./project-access-context\";\nimport { removeEndingSlash } from \"../formatters\";\n\n\nexport class ManifestParser {\n  private readonly manifest: DatasetAssetsManifest;\n  private readonly accessContext: ProjectFileAccessContext;\n\n  constructor(manifest: DatasetAssetsManifest, accessContext?: ProjectFileAccessContext) {\n    this.manifest = manifest;\n    this.accessContext = accessContext;\n  }\n\n  private get files(): Array<FileEntry> {\n    return this.manifest?.files ?? [];\n  }\n\n  /**\n   * Generates asset objects from the manifest, optionally including folder entries.\n   */\n  public generateAssets(generateFolders = false): Assets {\n    const domain = removeEndingSlash(this.manifest?.domain);\n    const assets = new Assets();\n\n    for (const file of this.files) {\n      assets.push(new File(domain, file.path, file.size, file.metadata, this.accessContext));\n    }\n\n    // Optionally add folder entries\n    if (generateFolders) {\n      assets.push(...this.generateFolderAssets(assets, domain));\n    }\n\n    return assets;\n  }\n\n  // Create folder entries, useful for visualizing folders as items in a file browser\n  private generateFolderAssets(assets: Assets, domain: string): Folder[] {\n    const folderSet = new Set<string>();\n\n    // Collect all unique folder paths\n    for (const asset of assets) {\n      const parts = asset.path.split('/').filter(p => p.length > 0);\n      let currentPath = '';\n      for (const part of parts) {\n        currentPath = currentPath ? `${currentPath}/${part}` : part;\n        folderSet.add(currentPath);\n      }\n    }\n\n    // Create Folder objects from unique paths\n    return Array.from(folderSet)\n      .map(folderPath => {\n        const name = folderPath.substring(folderPath.lastIndexOf('/') + 1);\n        const parentPath = folderPath.includes('/') ? folderPath.substring(0, folderPath.lastIndexOf('/')) : '';\n        return new Folder(folderPath, name, parentPath, domain);\n      });\n  }\n}\n","\n/**\n * Returns the parent directory of a given file path.\n */\nexport function getParentPath(path: string): string {\n  return path.split(\"/\").slice(0, -1).join(\"/\") ?? \"\"\n}\n","export class ApiError extends Error {\n  errors: string[];\n\n  constructor(message: string, errors: string[]) {\n    super(message);\n    this.errors = errors;\n  }\n}\n","import { Middleware, ResponseContext } from \"@cirrobio/api-client\";\nimport { ApiError } from \"./error\";\n\nexport class PortalErrorHandler implements Middleware {\n  async post(context: ResponseContext): Promise<Response | void> {\n    const { response } = context;\n    if (response && (response.status >= 200 && response.status < 300)) {\n      return response;\n    }\n\n    // Handle Error\n    let errorMessage: string;\n    const errors = [];\n    try {\n      const err = await response.json();\n      console.warn(err);\n      if ('errorDetail' in err) {\n        errorMessage = err.errorDetail;\n        errors.push(err.errors.map((e: any) => e.message));\n      } else {\n        errorMessage = err.message;\n      }\n    } catch (ignore) {\n      errorMessage = \"Unknown Error\";\n    }\n    throw new ApiError(errorMessage, errors);\n  }\n}\n","import { PortalErrorHandler } from \"./error-handler\";\nimport { Configuration } from \"@cirrobio/api-client\";\n\ninterface GetConfigParams {\n  tokenGetter: () => Promise<string>;\n  basePath?: string;\n}\n\nexport const generateApiConfig = ({ basePath = \"/api\", tokenGetter}: GetConfigParams) => {\n  return new Configuration({\n    basePath,\n    accessToken: tokenGetter,\n    middleware: [\n      new PortalErrorHandler()\n    ],\n  });\n}\n","export class CurrentUser {\n  username: string;\n  /**\n   * The unique identifier for the user\n   */\n  sub: string\n\n  /**\n   * The time the user authenticated\n   */\n  authTime: Date;\n\n  /**\n   * The groups the user belongs to\n   */\n  groups: string[];\n\n  static fromCognitoUser(idTokenPayload: Record<string, any>): CurrentUser {\n    return {\n      username: idTokenPayload[\"cognito:username\"] ?? idTokenPayload.username,\n      sub: idTokenPayload.sub,\n      authTime: new Date(idTokenPayload.auth_time * 1000),\n      groups: idTokenPayload[\"cognito:groups\"] ?? [],\n    };\n  }\n}\n","import { SystemInfoResponse } from \"@cirrobio/api-client\";\nimport { AuthenticationProvider } from \"./authentication-provider\";\nimport { CurrentUser } from \"./current-user\";\n\n\nexport class StaticTokenAuthProvider implements AuthenticationProvider {\n  constructor(\n    readonly token: string\n  ) {\n  }\n\n  public configure(_ignore: SystemInfoResponse): void {\n    console.log('StaticTokenAuthProvider loaded');\n  }\n\n  public async getAccessToken() {\n    return this.token;\n  }\n\n  public async getCurrentUser() {\n    const accessToken = await this.getAccessToken();\n    const parsedToken = JSON.parse(atob(accessToken.split('.')[1]));\n    return CurrentUser.fromCognitoUser(parsedToken);\n  }\n\n  public forceRefresh(): Promise<void> {\n    return Promise.resolve();\n  }\n}\n","import {\n  AuditApi,\n  BillingApi,\n  ComputeEnvironmentApi,\n  Configuration,\n  DatasetsApi,\n  ExecutionApi,\n  FileApi,\n  GovernanceApi,\n  MetadataApi,\n  NotebooksApi,\n  ProcessesApi,\n  ProjectRequestsApi,\n  ProjectsApi,\n  ReferencesApi,\n  SharingApi,\n  SystemApi,\n  ToolsApi,\n  UsersApi\n} from \"@cirrobio/api-client\";\nimport { generateApiConfig } from \"../api/config\";\n\ninterface DataServiceParams {\n  tokenGetter: () => Promise<string>;\n  basePath?: string;\n}\n\nexport class DataService {\n  private readonly apiConfig: Configuration;\n\n  private readonly _auditApi: AuditApi;\n  private readonly _billingApi: BillingApi;\n  private readonly _computeEnvironmentApi: ComputeEnvironmentApi;\n  private readonly _datasetsApi: DatasetsApi;\n  private readonly _executionApi: ExecutionApi;\n  private readonly _fileApi: FileApi;\n  private readonly _governanceApi: GovernanceApi;\n  private readonly _metadataApi: MetadataApi;\n  private readonly _notebooksApi: NotebooksApi;\n  private readonly _processesApi: ProcessesApi;\n  private readonly _projectRequestsApi: ProjectRequestsApi;\n  private readonly _projectsApi: ProjectsApi;\n  private readonly _referencesApi: ReferencesApi;\n  private readonly _sharingApi: SharingApi;\n  private readonly _systemApi: SystemApi;\n  private readonly _toolsApi: ToolsApi;\n  private readonly _usersApi: UsersApi;\n\n  constructor({ tokenGetter, basePath = \"/api\" }: DataServiceParams) {\n    this.apiConfig = generateApiConfig({ basePath, tokenGetter });\n\n    this._auditApi = new AuditApi(this.apiConfig);\n    this._billingApi = new BillingApi(this.apiConfig);\n    this._computeEnvironmentApi = new ComputeEnvironmentApi(this.apiConfig);\n    this._datasetsApi = new DatasetsApi(this.apiConfig);\n    this._executionApi = new ExecutionApi(this.apiConfig);\n    this._fileApi = new FileApi(this.apiConfig);\n    this._governanceApi = new GovernanceApi(this.apiConfig);\n    this._metadataApi = new MetadataApi(this.apiConfig);\n    this._notebooksApi = new NotebooksApi(this.apiConfig);\n    this._processesApi = new ProcessesApi(this.apiConfig);\n    this._projectRequestsApi = new ProjectRequestsApi(this.apiConfig);\n    this._projectsApi = new ProjectsApi(this.apiConfig);\n    this._referencesApi = new ReferencesApi(this.apiConfig);\n    this._sharingApi = new SharingApi(this.apiConfig);\n    this._systemApi = new SystemApi(this.apiConfig);\n    this._toolsApi = new ToolsApi(this.apiConfig);\n    this._usersApi = new UsersApi(this.apiConfig);\n  }\n\n  get audit(): AuditApi {\n    return this._auditApi;\n  }\n  get billing(): BillingApi {\n    return this._billingApi;\n  }\n  get computeEnvironments(): ComputeEnvironmentApi {\n    return this._computeEnvironmentApi;\n  }\n  get datasets(): DatasetsApi {\n    return this._datasetsApi;\n  }\n  get execution(): ExecutionApi {\n    return this._executionApi;\n  }\n  get file(): FileApi {\n    return this._fileApi;\n  }\n  get governance(): GovernanceApi {\n    return this._governanceApi;\n  }\n  get metadata(): MetadataApi {\n    return this._metadataApi;\n  }\n  get notebooks(): NotebooksApi {\n    return this._notebooksApi;\n  }\n  get processes(): ProcessesApi {\n    return this._processesApi;\n  }\n  get projectRequests(): ProjectRequestsApi {\n    return this._projectRequestsApi;\n  }\n  get projects(): ProjectsApi {\n    return this._projectsApi;\n  }\n  get references(): ReferencesApi {\n    return this._referencesApi;\n  }\n  get sharing(): SharingApi {\n    return this._sharingApi;\n  }\n  get system(): SystemApi {\n    return this._systemApi;\n  }\n  get tools(): ToolsApi {\n    return this._toolsApi;\n  }\n  get users(): UsersApi {\n    return this._usersApi;\n  }\n}\n","/**\n * Extracts a value from an object using the json path notation, i.e. $.test.id\n * @param path JSON path to the value\n * @param obj Object to extract the value from\n */\nexport function extractFromObject(path: string, obj: object): any {\n  const pathParts = path.slice(2).split('.')\n  return pathParts.reduce(function(o, k) {\n    return o && o[k];\n  }, obj);\n}\n","/**\n * Ignores dangling promise rejections.\n * @param err The error to ignore.\n */\nexport function handlePromiseError(err): void {\n  console.warn(err);\n}\n","/**\n * Download a blob as a file with the specified file name.\n */\nexport function downloadBlob(blob: Blob, fileName: string): void {\n  const url = window.URL.createObjectURL(blob);\n  const a = document.createElement('a');\n  a.href = url;\n  a.download = fileName;\n  a.click();\n}\n\n/**\n * Downloads the specified content as a file with the specified file name and type.\n */\nexport function downloadContent(content: any, fileName: string, fileType = 'text/plain'): void {\n  const blob = new Blob([content], { type: fileType });\n  downloadBlob(blob, 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package/dist/index.js

@@ -272,7 +272,8 @@ function uploadFile({ bucket, path, file, credentials, metadata }) {
         Key: path,
         Body: file,
         ContentType: file.type,
-        Metadata: metadata
+        Metadata: metadata,
+        ChecksumType: "FULL_OBJECT"
     };
     return new libStorage.Upload({
         client: createS3Client(credentials),

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":["../src/file/extensions.fn.ts","../src/file/util/credentials-mutex.so.ts","../src/file/util/s3-client.ts","../src/file/util/s3-utils.ts","../src/file/actions/sign-url.fn.ts","../src/util/get-resource-name.ts","../src/file/shared.ts","../src/file/file.service.ts","../src/file/actions/delete.fn.ts","../src/file/actions/upload.fn.ts","../src/file/project-access-context.ts","../src/file/models/file-object.model.ts","../src/file/calculate-size.ts","../src/formatters/json-pretty-print.ts","../src/formatters/bytes-to-string.ts","../src/formatters/normalize-date.ts","../src/formatters/normalize-string.ts","../src/formatters/slash.ts","../src/formatters/to-date-format.ts","../src/formatters/to-title-case.ts","../src/formatters/to-friendly-name.ts","../src/formatters/to-money.ts","../src/formatters/to-pascal-case.ts","../src/file/models/assets.ts","../src/file/models/folder.ts","../src/file/models/file.ts","../src/file/manifest-parser.ts","../src/file/util/get-parent.fn.ts","../src/api/error.ts","../src/api/error-handler.ts","../src/api/config.ts","../src/auth/current-user.ts","../src/auth/static-token-auth.ts","../src/data/data.service.ts","../src/util/extract-from-object.ts","../src/util/handle-promise.ts","../src/util/download.ts"],"sourcesContent":["\n/**\n * An array of file extensions that can be rendered in a genome viewer\n */\nexport const FILE_TRACK_ANNOTATION = ['bed', 'bed.gz', 'gtf', 'gtf.gz'];\nexport const FILE_TRACK_ALIGNMENTS = ['cram', 'cram.gz'];  // TODO: put back bam\nexport const FILE_TRACK_VARIANT = ['vcf', 'vcf.gz'];\nexport const FILE_TRACK_WIG = ['wig', 'wig.gz', 'bw', 'bw.gz', 'bigwig', 'bigwig.gz'];\nexport const FILE_TRACK_SEG = ['seg', 'seg.gz'];\nexport const FILE_TRACK_INDEX_EXTENSIONS = ['tbi', 'bai', 'crai', 'csi'];\nexport const FILE_VITESSCE_EXTENSIONS = ['hdf5', 'h5ad', 'loom'];\nexport const FILE_TRACK_EXTENSIONS_NO_INDEX = [\n    ...FILE_TRACK_ANNOTATION,\n    ...FILE_TRACK_ALIGNMENTS,\n    ...FILE_TRACK_VARIANT,\n    ...FILE_TRACK_WIG,\n    ...FILE_TRACK_SEG\n];\nexport const FILE_TRACK_EXTENSIONS = [\n    ...FILE_TRACK_EXTENSIONS_NO_INDEX,\n    ...FILE_TRACK_INDEX_EXTENSIONS\n]\n\n\nexport const FILE_BROWSER_EXTENSIONS = ['html', 'pdf'];\n\n\n/**\n * An array of file extensions that are protein structure files.\n */\nexport const FILE_PROTEIN_STRUCTURE_EXTENSIONS = ['pdb', 'pdb.gz', 'cif', 'cif.gz', 'ent', 'ent.gz', 'mmtf', 'mmtf.gz'];\n/**\n * An array of file extensions that are considered tabular files.\n */\nexport const FILE_DSV_EXTENSIONS = ['tab', 'csv', 'tsv', 'dsv'];\n/**\n * An array of file extensions that contain genomic sequence content.\n */\nexport const FILE_TXT_GENOMICS_EXTENSIONS = ['fasta', 'fna', 'fsa', 'fa', 'fastp', 'fastq', 'faa', 'gbk', 'gff', 'vcf', 'seq'];\n\n/**\n * An array of file extensions that are considered TXT files.\n */\nexport const FILE_TXT_EXTENSIONS = ['txt', 'log', 'yml', 'cfg', 'config', 'xml', 'yaml', ...FILE_DSV_EXTENSIONS, ...FILE_TXT_GENOMICS_EXTENSIONS];\n\n\n/**\n * An array of file extensions that are considered image files.\n */\nexport const FILE_IMAGE_EXTENSIONS = ['jpg', 'jpeg', 'png', 'svg'];\n\n/**\n * An array of file extensions that are considered OME (Open Microscopy Environment) files.\n */\nexport const FILE_OME_EXTENSIONS = ['tif', 'ome.tif', 'ome.tiff', 'ome.tif.gz', 'ome.tiff.gz'];\n\n/**\n * An array of file extensions that can be opened in the browser.\n * Includes common document formats such as HTML, PDF, and JSON, as well as image, DSV, TXT, and OME file formats.\n */\nexport const FILE_EXTENSIONS_TO_OPEN = ['html', 'pdf', 'json', 'fcs',\n    ...FILE_IMAGE_EXTENSIONS,\n    ...FILE_TXT_EXTENSIONS,\n    ...FILE_TRACK_EXTENSIONS,\n    ...FILE_PROTEIN_STRUCTURE_EXTENSIONS\n];\n\n\n/**\n * Checks if a file has an extension that matches one in the provided list.\n * @param filePath The file to check the extension of.\n * @param extensions A list of file endings to check the file against.\n * @returns True or false if the file has an ending in the extensions list.\n */\nexport function matchesExtension(filePath: string, extensions: string[]): boolean {\n    filePath = filePath.toLowerCase();\n\n    // Decompress the filePath if it ends with .gz\n    if (filePath.endsWith('.gz')) {\n        filePath = filePath.slice(0, -3);  // remove the .gz extension\n    }\n\n    // Now, get the extension of the file\n    const fileExtension = filePath.slice(filePath.lastIndexOf('.') + 1);\n\n    // Check if the fileExtension is in the list of extensions\n    return extensions.includes(fileExtension);\n}\n","import { AWSCredentials } from '@cirrobio/api-client';\n\nclass Mutex<T> {\n  private mutex = Promise.resolve();\n\n  lock(): PromiseLike<() => void> {\n    let begin: (unlock: () => void) => void = () => { /* Do nothing */ };\n\n    this.mutex = this.mutex.then(() => new Promise(begin));\n\n    return new Promise((res) => {\n      begin = res;\n    });\n  }\n\n  async dispatch(fn: (() => T) | (() => PromiseLike<T>)): Promise<T> {\n    const unlock = await this.lock();\n    try {\n      return await Promise.resolve(fn());\n    } finally {\n      unlock();\n    }\n  }\n}\n\n/**\n * A mutex to ensure that only one request for credentials is made at a time.\n */\nexport const credentialsMutex = new Mutex<AWSCredentials>();\n/**\n * A cache of credentials to avoid making multiple requests for the same credentials.\n */\nexport const credentialsCache: Map<string, AWSCredentials> = new Map<string, AWSCredentials>();\n","import { S3Client } from \"@aws-sdk/client-s3\";\nimport { AWSCredentials } from \"@cirrobio/api-client\";\n\nconst clientCache = new Map<string, S3Client>();\n\n/**\n * Creates an S3 client using the provided credentials.\n */\nexport function createS3Client(credentials: AWSCredentials): S3Client {\n  const cacheKey = `${credentials.accessKeyId}-${credentials.region}`;\n  const cachedClient = clientCache.get(cacheKey);\n  if (cachedClient) {\n    return cachedClient;\n  }\n  const newClient = new S3Client({\n    credentials: {\n      accessKeyId: credentials.accessKeyId,\n      secretAccessKey: credentials.secretAccessKey,\n      sessionToken: credentials.sessionToken,\n    },\n    region: credentials.region,\n    useDualstackEndpoint: true,\n  });\n  clientCache.set(cacheKey, newClient);\n  return newClient;\n}\n","/**\n * Converts an S3 URI to a bucket and key\n */\nexport function s3UriToParams(uri: string): { Bucket: string, Key: string } {\n  const matches = /^s3:\\/\\/([^/]+)\\/(.+)$/.exec(uri);\n  if (!matches) {\n    throw new Error(`Received invalid uri: '${uri}'`);\n  }\n  return {\n    Bucket: matches[1],\n    Key: matches[2],\n  };\n}\n\n","import { AWSCredentials } from \"@cirrobio/api-client\";\nimport { GetObjectCommand, GetObjectCommandInput } from \"@aws-sdk/client-s3\";\nimport { getSignedUrl as getSignedUrlInternal } from \"@aws-sdk/s3-request-presigner\";\nimport { createS3Client } from \"../util/s3-client\";\nimport { s3UriToParams } from \"../util/s3-utils\";\n\nexport interface GetFileUrlParams extends GetSignedUrlOptions {\n  url: string;\n  credentials?: AWSCredentials;\n}\n\nexport interface GetSignedUrlOptions {\n  download?: boolean;\n  gzip?: boolean;\n  timeout?: number;\n  filename?: string;\n}\n\n/**\n * Get a signed URL for a file in S3 given its S3 URI.\n * Defaults to a 5 minute timeout.\n */\nexport function getSignedUrl({ url, credentials, ...params }: GetFileUrlParams): Promise<string> {\n  const client = createS3Client(credentials);\n  const { Bucket, Key } = s3UriToParams(url);\n  const fileName = params.filename ?? Key.split('/').pop();\n  const args: GetObjectCommandInput = { Bucket, Key };\n  if (params?.download) {\n    args.ResponseContentDisposition = `attachment; filename=\"${fileName}\"`\n  }\n  if (params?.gzip) {\n    args.ResponseContentEncoding = 'gzip'\n  }\n  const command = new GetObjectCommand(args);\n  return getSignedUrlInternal(client, command, { expiresIn: 60 * (params?.timeout ?? 5) });\n}\n","\nconst resourcePrefix = 'project-';\n\nexport function getResourceName(projectId: string): string {\n  return `${resourcePrefix}${projectId}`;\n}\n\n","import { getResourceName } from \"../util/get-resource-name\";\n\n/**\n * Get the S3 bucket name for a project.\n * Will be deprecated in the future, use domain from manifest instead.\n */\nexport function getProjectS3Bucket(projectId: string): string {\n  return getResourceName(projectId)\n}\n","import { AWSCredentials, GenerateProjectFileAccessTokenRequest, ProjectAccessType } from \"@cirrobio/api-client\";\nimport { ProjectFileAccessContext } from \"./project-access-context\";\nimport { credentialsCache, credentialsMutex } from \"./util/credentials-mutex.so\";\nimport { GetFileUrlParams, getSignedUrl, GetSignedUrlOptions } from \"./actions/sign-url.fn\";\nimport { getProjectS3Bucket } from \"./shared\";\nimport { DownloadableFile } from \"./models/file-object.model\";\n\nexport interface IFileCredentialsApi {\n  generateProjectFileAccessToken: (params: GenerateProjectFileAccessTokenRequest) => Promise<AWSCredentials>;\n}\n\n/**\n * Service for viewing files in Cirro\n *  currently this only operates on files within a project\n */\nexport class FileService {\n  constructor(\n    private readonly fileCredsApi: IFileCredentialsApi\n  ) {}\n\n  /**\n   * Get contents of a file\n   */\n  async getProjectFile(file: DownloadableFile): Promise<Response> {\n    const url = await this.getSignedUrlFromProjectFile(file);\n    return fetch(url);\n  }\n\n  /**\n   * Get a signed URL for a file\n   */\n  async getSignedUrlFromProjectFile(file: DownloadableFile, params?: GetSignedUrlOptions): Promise<string> {\n    const credentials = await this.getProjectAccessCredentials(file.fileAccessContext);\n    const _params: GetFileUrlParams = {\n      ...params,\n      filename: file.name,\n      url: file.url,\n      credentials,\n    };\n    return getSignedUrl(_params);\n  }\n\n  /**\n   * Get a signed URL for a file given a path\n   */\n  async getSignedUrlFromProjectPath(fileAccessContext: ProjectFileAccessContext, path: string, params?: GetSignedUrlOptions): Promise<string> {\n    const credentials = await this.getProjectAccessCredentials(fileAccessContext);\n    const _params: GetFileUrlParams = {\n      ...params,\n      filename: path.split('/').pop(),\n      url: `s3://${getProjectS3Bucket(fileAccessContext.project.id)}/${path}`,\n      credentials,\n    };\n    return getSignedUrl(_params);\n  }\n\n  /**\n   * Get credentials for accessing a project file\n   */\n  async getProjectAccessCredentials(fileAccessContext: ProjectFileAccessContext): Promise<AWSCredentials> {\n    const accessType = fileAccessContext.fileAccessRequest.accessType;\n    // Special case for project download, since we can cache the credentials\n    if (accessType === ProjectAccessType.ProjectDownload || accessType === ProjectAccessType.SharedDatasetDownload) {\n      return this.getProjectReadCredentials(fileAccessContext);\n    }\n    return this.fileCredsApi.generateProjectFileAccessToken({ projectId: fileAccessContext.project.id, projectFileAccessRequest: fileAccessContext.fileAccessRequest });\n  }\n\n  private async getProjectReadCredentials(fileAccessContext: ProjectFileAccessContext): Promise<AWSCredentials> {\n    const projectId = fileAccessContext.project.id;\n    // Append datasetId to cache key for shared dataset downloads since we need to generate a new token for each dataset\n    let cacheKey = projectId;\n    if (fileAccessContext.fileAccessRequest.accessType === ProjectAccessType.SharedDatasetDownload) {\n      cacheKey = `${projectId}-${fileAccessContext.fileAccessRequest.datasetId}`;\n    }\n\n    return credentialsMutex.dispatch(async () => {\n      const cachedCredentials = credentialsCache.get(cacheKey);\n      const expirationTime = cachedCredentials ? cachedCredentials?.expiration : null;\n      const fetchNewCredentials = !expirationTime || expirationTime < new Date();\n      if (fetchNewCredentials) {\n        const projectFileAccessRequest = fileAccessContext.fileAccessRequest;\n        const credentials = await this.fileCredsApi.generateProjectFileAccessToken({ projectId, projectFileAccessRequest });\n        credentialsCache.set(cacheKey, credentials);\n        return credentials;\n      }\n      return cachedCredentials;\n    });\n  }\n}\n","import { AWSCredentials } from \"@cirrobio/api-client\";\nimport { DeleteObjectCommand } from \"@aws-sdk/client-s3\";\nimport { s3UriToParams } from \"../util/s3-utils\";\nimport { createS3Client } from \"../util/s3-client\";\n\nexport interface DeleteFileParams {\n  url: string;\n  credentials: AWSCredentials;\n}\n\n/**\n * Delete a file from S3 given its URL and credentials.\n */\nexport async function deleteFile({ url, credentials }: DeleteFileParams): Promise<void> {\n  const { Bucket, Key } = s3UriToParams(url);\n  const cmd = new DeleteObjectCommand({ Bucket, Key });\n  await createS3Client(credentials).send(cmd);\n}\n","import { Upload } from \"@aws-sdk/lib-storage\";\nimport { AWSCredentials } from '@cirrobio/api-client';\nimport { createS3Client } from \"../util/s3-client\";\nimport { PutObjectCommandInput } from \"@aws-sdk/client-s3\";\n\nexport interface UploadFileParams {\n  bucket: string;\n  path: string;\n  file: File;\n  credentials: AWSCredentials;\n  metadata?: Record<string, string>;\n}\n\n/**\n * Upload a file to S3\n */\nexport function uploadFile({ bucket, path, file, credentials, metadata }: UploadFileParams): Upload {\n  const params: PutObjectCommandInput = {\n    Bucket: bucket,\n    Key: path,\n    Body: file,\n    ContentType: file.type,\n    Metadata: metadata\n  };\n  return new Upload({\n    client: createS3Client(credentials),\n    queueSize: 4,\n    params,\n  });\n}\n\n","import { ProjectAccessType, DatasetDetail, ProjectFileAccessRequest, Project } from \"@cirrobio/api-client\";\n\ntype ProjectIdentifiable = Pick<Project, 'id'>;\n\n/**\n * Helper class to encapsulate the file access for a project.\n */\nexport class ProjectFileAccessContext {\n  constructor(\n    readonly project: ProjectIdentifiable,\n    readonly dataset: DatasetDetail,\n    readonly fileAccessRequest: ProjectFileAccessRequest\n  ) {\n  }\n\n  static projectDownload(project: ProjectIdentifiable): ProjectFileAccessContext {\n    const request: ProjectFileAccessRequest = { accessType: ProjectAccessType.ProjectDownload };\n    return new ProjectFileAccessContext(project, null, request);\n  }\n\n  static datasetDownload(project: ProjectIdentifiable, dataset: DatasetDetail): ProjectFileAccessContext {\n    const accessType = dataset.share ? ProjectAccessType.SharedDatasetDownload : ProjectAccessType.ProjectDownload;\n    const request: ProjectFileAccessRequest = { accessType, datasetId: dataset.id };\n    return new ProjectFileAccessContext(project, dataset, request);\n  }\n}\n","import { ProjectFileAccessContext } from \"../project-access-context\";\n\nexport enum FileSystemObjectType {\n  FILE = 'file',\n  FOLDER = 'folder'\n}\n\n/**\n * Represents a file that can be downloaded\n */\nexport interface DownloadableFile {\n  url: string;\n  name?: string;\n  fileAccessContext: ProjectFileAccessContext;\n}\n\n/**\n * Represents a file in Cirro\n */\nexport interface FileSystemObject extends DownloadableFile {\n  /**\n   * Unique Id For Object\n   */\n  id: string;\n  /**\n   * Object S3 Url\n   */\n  url: string;\n  /**\n   * Object Path\n   */\n  path: string;\n  /**\n   * Object Name\n   */\n  name: string;\n  /**\n   * Object Size\n   */\n  size: number;\n  /**\n   * Object Kind (PNG, TXT)\n   */\n  kind: string;\n  /**\n   * Object Type (File or Folder)\n   */\n  type: FileSystemObjectType;\n  /**\n   * Metadata\n   */\n  metadata?: Record<string, any>;\n  /**\n   * Access context\n   */\n  fileAccessContext: ProjectFileAccessContext;\n}\n","import { FileSystemObject } from \"./models/file-object.model\";\n\n/**\n * Calculate the total size of all files in a directory.\n * @param files - An array of FileSystemObject representing the files in the directory.\n * @return The total size of all files in bytes.\n */\nexport function calculateTotalSize(files: Array<FileSystemObject>): number {\n  let totalSize = 0;\n  for (const file of files) {\n    totalSize += file.size;\n  }\n  return totalSize;\n}\n","/**\n * Pretty prints a JSON object with the specified indentation level.\n * @param obj JSON object to be pretty printed.\n * @param indentLevel Number of spaces to use for indentation.\n */\nexport function jsonPrettyPrint(obj: object, indentLevel=2): string {\n  return JSON.stringify(obj, null, indentLevel);\n}\n","/**\n * Format bytes as human-readable text.\n * @param bytes Number of bytes.\n * @param si True to use metric(SI) units, aka powers of 1000. False to use\n * binary(IEC), aka powers of 1024.\n   * @param dp Number of decimal places to display.\n *\n * @return Formatted string.\n */\nexport function bytesToString(bytes, si = false, dp = 1): string {\n  const thresh = si ? 1000 : 1024;\n\n  if (Math.abs(bytes) < thresh) {\n    return `${bytes} B`;\n  }\n\n  const units = si\n    ? ['kB', 'MB', 'GB', 'TB', 'PB', 'EB', 'ZB', 'YB']\n    : ['KiB', 'MiB', 'GiB', 'TiB', 'PiB', 'EiB', 'ZiB', 'YiB'];\n  let u = -1;\n  const r = 10 ** dp;\n\n  do {\n    bytes /= thresh;\n    ++u;\n  } while (\n    Math.round(Math.abs(bytes) * r) / r >= thresh\n    && u < units.length - 1\n    );\n\n  return `${bytes.toFixed(dp)} ${units[u]}`;\n}\n","/**\n * Normalizes a date to UTC by adjusting for the timezone offset.\n * Useful when you are working with dates that may not include time information.\n * @param date\n */\nexport function normalizeDate(date: Date | string | undefined | null): Date {\n  if (!date) throw new Error(\"Attempt to normalize undefined\");\n  if (!(date instanceof Date)) date = new Date(date);\n  return new Date(date.getTime() - date.getTimezoneOffset() * -60000);\n}\n","/**\n * Normalize a string by trimming it and returning null if it is empty.\n * @param input The string to normalize.\n */\nexport function normalizeString(input: string): string {\n  if (!input?.trim()) return null;\n  return input.trim();\n}\n","/**\n * Removes the starting slash from a path.\n * @param path Input path\n */\nexport function removeStartingSlash(path: string): string {\n  if (!path) return path;\n  if (path.startsWith('./')) return path.substring(2);\n  if (path.startsWith('/')) return path.substring(1);\n  return path;\n}\n\n/**\n * Removes the ending slash from a path.\n * @param path Input path\n */\nexport function removeEndingSlash(path: string): string {\n  return path?.endsWith('/') ? path.slice(0, -1) : path;\n}\n","const dateFormat = new Intl.DateTimeFormat('en-US', { month: '2-digit', day: '2-digit', year: '2-digit' });\n\n/**\n * Converts a date string or Date object to MM/DD/YY date string.\n * Ex., \"2023-10-01\" -> \"10/01/23\"\n * @param date Input date string or Date object.\n */\nexport function toDateFormat(date: string | Date): string {\n  if (!date) return null;\n  const d: Date = (typeof date === 'string') ? new Date(date) : date\n  return dateFormat.format(d);\n}\n","/**\n * Converts a string to Title case.\n * Ex., \"hello world\" -> \"Hello world\"\n * @param value\n */\nexport function toTitleCase(value: string): string {\n  if (!value) return null;\n  return value[0].toUpperCase() + value.slice(1).toLowerCase();\n}\n","import { toTitleCase } from './to-title-case';\n\n/**\n * Converts a field name to a more human-readable format.\n * Ex., \"helloWorld\" -> \"Hello World\"\n * @param value The value to convert.\n */\nexport function toFriendlyName(value: string): string {\n  let _value = value.split(/(?=[A-Z])/).join(' ');\n  _value = _value.split('_').join(' ');\n  _value = _value.split('|').join(' ');\n  _value = _value.replace(/ +/g, ' ');\n  return toTitleCase(_value);\n}\n","const money = new Intl.NumberFormat('en-US', {\n  style: 'currency',\n  currency: 'USD',\n});\n\n/**\n * Converts a number or bigint to a formatted money string.\n * Ex., 1234.56 -> $1,234.56\n * @param value Input number or bigint value.\n */\nexport function toMoney(value: number | bigint): string {\n  return money.format(value as number);\n}\n","/**\n * Converts a string to PascalCase.\n * Ex., \"hello world\" -> \"HelloWorld\"\n * @param value The string to convert.\n */\nexport function toPascalCase(value: string): string {\n  return value.replace(/(\\w)(\\w*)/g, (g0, g1, g2) => g1.toUpperCase() + g2.toLowerCase());\n}\n","import { calculateTotalSize } from \"../calculate-size\";\nimport { bytesToString } from \"../../formatters\";\nimport { FileSystemObject } from \"./file-object.model\";\n\nexport class Assets extends Array<FileSystemObject> {\n  private _totalSize: string;\n  private _totalSizeBytes: number;\n\n  // Total size of all files in human-readable format\n  get totalSize(): string {\n    if (!this._totalSize) {\n      this.calculateSize();\n    }\n    return this._totalSize;\n  }\n\n  get totalSizeBytes(): number {\n    if (!this._totalSizeBytes) {\n      this.calculateSize();\n    }\n    return this._totalSizeBytes;\n  }\n  private calculateSize(): void {\n    this._totalSizeBytes = calculateTotalSize(this);\n    this._totalSize = bytesToString(this._totalSizeBytes)\n  }\n}\n","import { v4 as uuidv4 } from 'uuid';\nimport { FileSystemObject, FileSystemObjectType } from \"./file-object.model\";\n\nexport class Folder implements FileSystemObject {\n  readonly id: string;\n  readonly url: string;\n  readonly path: string;\n  readonly name: string;\n  readonly domain: string;\n  readonly kind = 'Folder';\n  readonly fileAccessContext = null;\n  readonly size = 0;\n  readonly type = FileSystemObjectType.FOLDER;\n\n  constructor(url: string, name: string, path: string, domain: string) {\n    this.id = uuidv4();\n    this.url = url;\n    this.name = name;\n    this.path = path;\n    this.domain = domain;\n  }\n}\n","import { FileSystemObject, FileSystemObjectType } from \"./file-object.model\";\nimport { ProjectFileAccessContext } from \"../project-access-context\";\nimport { v4 as uuidv4 } from 'uuid';\n\nexport class File implements FileSystemObject {\n  readonly id: string;\n  readonly url: string\n  readonly size: number;\n  readonly path: string;\n  readonly name: string;\n  readonly metadata: Record<string, any>;\n  readonly fileAccessContext: ProjectFileAccessContext;\n\n  get type() {\n    return FileSystemObjectType.FILE;\n  }\n\n  get kind() {\n    return this.path.slice(this.\n    path.lastIndexOf('.') + 1);\n  }\n\n  constructor(domain: string, file: string, size: number, metadata: Record<string, any>, accessContext: ProjectFileAccessContext) {\n    this.id = uuidv4();\n    this.url = `${domain}/${file}`;\n    this.size = size;\n    this.metadata = metadata;\n    this.fileAccessContext = accessContext;\n\n    const fileFolderIdx = file.lastIndexOf('/');\n    if (fileFolderIdx === -1) {\n      this.path = '';\n      this.name = file;\n    } else {\n      this.path = file.substring(0, fileFolderIdx);\n      this.name = file.substring(fileFolderIdx + 1);\n    }\n  }\n}\n","import { DatasetAssetsManifest, FileEntry } from '@cirrobio/api-client';\nimport { Assets } from \"./models/assets\";\nimport { Folder } from \"./models/folder\";\nimport { File } from \"./models/file\";\nimport { ProjectFileAccessContext } from \"./project-access-context\";\nimport { removeEndingSlash } from \"../formatters\";\n\n\nexport class ManifestParser {\n  private readonly manifest: DatasetAssetsManifest;\n  private readonly accessContext: ProjectFileAccessContext;\n\n  constructor(manifest: DatasetAssetsManifest, accessContext?: ProjectFileAccessContext) {\n    this.manifest = manifest;\n    this.accessContext = accessContext;\n  }\n\n  private get files(): Array<FileEntry> {\n    return this.manifest?.files ?? [];\n  }\n\n  /**\n   * Generates asset objects from the manifest, optionally including folder entries.\n   */\n  public generateAssets(generateFolders = false): Assets {\n    const domain = removeEndingSlash(this.manifest?.domain);\n    const assets = new Assets();\n\n    for (const file of this.files) {\n      assets.push(new File(domain, file.path, file.size, file.metadata, this.accessContext));\n    }\n\n    // Optionally add folder entries\n    if (generateFolders) {\n      assets.push(...this.generateFolderAssets(assets, domain));\n    }\n\n    return assets;\n  }\n\n  // Create folder entries, useful for visualizing folders as items in a file browser\n  private generateFolderAssets(assets: Assets, domain: string): Folder[] {\n    const folderSet = new Set<string>();\n\n    // Collect all unique folder paths\n    for (const asset of assets) {\n      const parts = asset.path.split('/').filter(p => p.length > 0);\n      let currentPath = '';\n      for (const part of parts) {\n        currentPath = currentPath ? `${currentPath}/${part}` : part;\n        folderSet.add(currentPath);\n      }\n    }\n\n    // Create Folder objects from unique paths\n    return Array.from(folderSet)\n      .map(folderPath => {\n        const name = folderPath.substring(folderPath.lastIndexOf('/') + 1);\n        const parentPath = folderPath.includes('/') ? folderPath.substring(0, folderPath.lastIndexOf('/')) : '';\n        return new Folder(folderPath, name, parentPath, domain);\n      });\n  }\n}\n","\n/**\n * Returns the parent directory of a given file path.\n */\nexport function getParentPath(path: string): string {\n  return path.split(\"/\").slice(0, -1).join(\"/\") ?? \"\"\n}\n","export class ApiError extends Error {\n  errors: string[];\n\n  constructor(message: string, errors: string[]) {\n    super(message);\n    this.errors = errors;\n  }\n}\n","import { Middleware, ResponseContext } from \"@cirrobio/api-client\";\nimport { ApiError } from \"./error\";\n\nexport class PortalErrorHandler implements Middleware {\n  async post(context: ResponseContext): Promise<Response | void> {\n    const { response } = context;\n    if (response && (response.status >= 200 && response.status < 300)) {\n      return response;\n    }\n\n    // Handle Error\n    let errorMessage: string;\n    const errors = [];\n    try {\n      const err = await response.json();\n      console.warn(err);\n      if ('errorDetail' in err) {\n        errorMessage = err.errorDetail;\n        errors.push(err.errors.map((e: any) => e.message));\n      } else {\n        errorMessage = err.message;\n      }\n    } catch (ignore) {\n      errorMessage = \"Unknown Error\";\n    }\n    throw new ApiError(errorMessage, errors);\n  }\n}\n","import { PortalErrorHandler } from \"./error-handler\";\nimport { Configuration } from \"@cirrobio/api-client\";\n\ninterface GetConfigParams {\n  tokenGetter: () => Promise<string>;\n  basePath?: string;\n}\n\nexport const generateApiConfig = ({ basePath = \"/api\", tokenGetter}: GetConfigParams) => {\n  return new Configuration({\n    basePath,\n    accessToken: tokenGetter,\n    middleware: [\n      new PortalErrorHandler()\n    ],\n  });\n}\n","export class CurrentUser {\n  username: string;\n  /**\n   * The unique identifier for the user\n   */\n  sub: string\n\n  /**\n   * The time the user authenticated\n   */\n  authTime: Date;\n\n  /**\n   * The groups the user belongs to\n   */\n  groups: string[];\n\n  static fromCognitoUser(idTokenPayload: Record<string, any>): CurrentUser {\n    return {\n      username: idTokenPayload[\"cognito:username\"] ?? idTokenPayload.username,\n      sub: idTokenPayload.sub,\n      authTime: new Date(idTokenPayload.auth_time * 1000),\n      groups: idTokenPayload[\"cognito:groups\"] ?? [],\n    };\n  }\n}\n","import { SystemInfoResponse } from \"@cirrobio/api-client\";\nimport { AuthenticationProvider } from \"./authentication-provider\";\nimport { CurrentUser } from \"./current-user\";\n\n\nexport class StaticTokenAuthProvider implements AuthenticationProvider {\n  constructor(\n    readonly token: string\n  ) {\n  }\n\n  public configure(_ignore: SystemInfoResponse): void {\n    console.log('StaticTokenAuthProvider loaded');\n  }\n\n  public async getAccessToken() {\n    return this.token;\n  }\n\n  public async getCurrentUser() {\n    const accessToken = await this.getAccessToken();\n    const parsedToken = JSON.parse(atob(accessToken.split('.')[1]));\n    return CurrentUser.fromCognitoUser(parsedToken);\n  }\n\n  public forceRefresh(): Promise<void> {\n    return Promise.resolve();\n  }\n}\n","import {\n  AuditApi,\n  BillingApi,\n  ComputeEnvironmentApi,\n  Configuration,\n  DatasetsApi,\n  ExecutionApi,\n  FileApi,\n  GovernanceApi,\n  MetadataApi,\n  NotebooksApi,\n  ProcessesApi,\n  ProjectRequestsApi,\n  ProjectsApi,\n  ReferencesApi,\n  SharingApi,\n  SystemApi,\n  ToolsApi,\n  UsersApi\n} from \"@cirrobio/api-client\";\nimport { generateApiConfig } from \"../api/config\";\n\ninterface DataServiceParams {\n  tokenGetter: () => Promise<string>;\n  basePath?: string;\n}\n\nexport class DataService {\n  private readonly apiConfig: Configuration;\n\n  private readonly _auditApi: AuditApi;\n  private readonly _billingApi: BillingApi;\n  private readonly _computeEnvironmentApi: ComputeEnvironmentApi;\n  private readonly _datasetsApi: DatasetsApi;\n  private readonly _executionApi: ExecutionApi;\n  private readonly _fileApi: FileApi;\n  private readonly _governanceApi: GovernanceApi;\n  private readonly _metadataApi: MetadataApi;\n  private readonly _notebooksApi: NotebooksApi;\n  private readonly _processesApi: ProcessesApi;\n  private readonly _projectRequestsApi: ProjectRequestsApi;\n  private readonly _projectsApi: ProjectsApi;\n  private readonly _referencesApi: ReferencesApi;\n  private readonly _sharingApi: SharingApi;\n  private readonly _systemApi: SystemApi;\n  private readonly _toolsApi: ToolsApi;\n  private readonly _usersApi: UsersApi;\n\n  constructor({ tokenGetter, basePath = \"/api\" }: DataServiceParams) {\n    this.apiConfig = generateApiConfig({ basePath, tokenGetter });\n\n    this._auditApi = new AuditApi(this.apiConfig);\n    this._billingApi = new BillingApi(this.apiConfig);\n    this._computeEnvironmentApi = new ComputeEnvironmentApi(this.apiConfig);\n    this._datasetsApi = new DatasetsApi(this.apiConfig);\n    this._executionApi = new ExecutionApi(this.apiConfig);\n    this._fileApi = new FileApi(this.apiConfig);\n    this._governanceApi = new GovernanceApi(this.apiConfig);\n    this._metadataApi = new MetadataApi(this.apiConfig);\n    this._notebooksApi = new NotebooksApi(this.apiConfig);\n    this._processesApi = new ProcessesApi(this.apiConfig);\n    this._projectRequestsApi = new ProjectRequestsApi(this.apiConfig);\n    this._projectsApi = new ProjectsApi(this.apiConfig);\n    this._referencesApi = new ReferencesApi(this.apiConfig);\n    this._sharingApi = new SharingApi(this.apiConfig);\n    this._systemApi = new SystemApi(this.apiConfig);\n    this._toolsApi = new ToolsApi(this.apiConfig);\n    this._usersApi = new UsersApi(this.apiConfig);\n  }\n\n  get audit(): AuditApi {\n    return this._auditApi;\n  }\n  get billing(): BillingApi {\n    return this._billingApi;\n  }\n  get computeEnvironments(): ComputeEnvironmentApi {\n    return this._computeEnvironmentApi;\n  }\n  get datasets(): DatasetsApi {\n    return this._datasetsApi;\n  }\n  get execution(): ExecutionApi {\n    return this._executionApi;\n  }\n  get file(): FileApi {\n    return this._fileApi;\n  }\n  get governance(): GovernanceApi {\n    return this._governanceApi;\n  }\n  get metadata(): MetadataApi {\n    return this._metadataApi;\n  }\n  get notebooks(): NotebooksApi {\n    return this._notebooksApi;\n  }\n  get processes(): ProcessesApi {\n    return this._processesApi;\n  }\n  get projectRequests(): ProjectRequestsApi {\n    return this._projectRequestsApi;\n  }\n  get projects(): ProjectsApi {\n    return this._projectsApi;\n  }\n  get references(): ReferencesApi {\n    return this._referencesApi;\n  }\n  get sharing(): SharingApi {\n    return this._sharingApi;\n  }\n  get system(): SystemApi {\n    return this._systemApi;\n  }\n  get tools(): ToolsApi {\n    return this._toolsApi;\n  }\n  get users(): UsersApi {\n    return this._usersApi;\n  }\n}\n","/**\n * Extracts a value from an object using the json path notation, i.e. $.test.id\n * @param path JSON path to the value\n * @param obj Object to extract the value from\n */\nexport function extractFromObject(path: string, obj: object): any {\n  const pathParts = path.slice(2).split('.')\n  return pathParts.reduce(function(o, k) {\n    return o && o[k];\n  }, obj);\n}\n","/**\n * Ignores dangling promise 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+{"version":3,"file":"index.js","sources":["../src/file/extensions.fn.ts","../src/file/util/credentials-mutex.so.ts","../src/file/util/s3-client.ts","../src/file/util/s3-utils.ts","../src/file/actions/sign-url.fn.ts","../src/util/get-resource-name.ts","../src/file/shared.ts","../src/file/file.service.ts","../src/file/actions/delete.fn.ts","../src/file/actions/upload.fn.ts","../src/file/project-access-context.ts","../src/file/models/file-object.model.ts","../src/file/calculate-size.ts","../src/formatters/json-pretty-print.ts","../src/formatters/bytes-to-string.ts","../src/formatters/normalize-date.ts","../src/formatters/normalize-string.ts","../src/formatters/slash.ts","../src/formatters/to-date-format.ts","../src/formatters/to-title-case.ts","../src/formatters/to-friendly-name.ts","../src/formatters/to-money.ts","../src/formatters/to-pascal-case.ts","../src/file/models/assets.ts","../src/file/models/folder.ts","../src/file/models/file.ts","../src/file/manifest-parser.ts","../src/file/util/get-parent.fn.ts","../src/api/error.ts","../src/api/error-handler.ts","../src/api/config.ts","../src/auth/current-user.ts","../src/auth/static-token-auth.ts","../src/data/data.service.ts","../src/util/extract-from-object.ts","../src/util/handle-promise.ts","../src/util/download.ts"],"sourcesContent":["\n/**\n * An array of file extensions that can be rendered in a genome viewer\n */\nexport const FILE_TRACK_ANNOTATION = ['bed', 'bed.gz', 'gtf', 'gtf.gz'];\nexport const FILE_TRACK_ALIGNMENTS = ['cram', 'cram.gz'];  // TODO: put back bam\nexport const FILE_TRACK_VARIANT = ['vcf', 'vcf.gz'];\nexport const FILE_TRACK_WIG = ['wig', 'wig.gz', 'bw', 'bw.gz', 'bigwig', 'bigwig.gz'];\nexport const FILE_TRACK_SEG = ['seg', 'seg.gz'];\nexport const FILE_TRACK_INDEX_EXTENSIONS = ['tbi', 'bai', 'crai', 'csi'];\nexport const FILE_VITESSCE_EXTENSIONS = ['hdf5', 'h5ad', 'loom'];\nexport const FILE_TRACK_EXTENSIONS_NO_INDEX = [\n    ...FILE_TRACK_ANNOTATION,\n    ...FILE_TRACK_ALIGNMENTS,\n    ...FILE_TRACK_VARIANT,\n    ...FILE_TRACK_WIG,\n    ...FILE_TRACK_SEG\n];\nexport const FILE_TRACK_EXTENSIONS = [\n    ...FILE_TRACK_EXTENSIONS_NO_INDEX,\n    ...FILE_TRACK_INDEX_EXTENSIONS\n]\n\n\nexport const FILE_BROWSER_EXTENSIONS = ['html', 'pdf'];\n\n\n/**\n * An array of file extensions that are protein structure files.\n */\nexport const FILE_PROTEIN_STRUCTURE_EXTENSIONS = ['pdb', 'pdb.gz', 'cif', 'cif.gz', 'ent', 'ent.gz', 'mmtf', 'mmtf.gz'];\n/**\n * An array of file extensions that are considered tabular files.\n */\nexport const FILE_DSV_EXTENSIONS = ['tab', 'csv', 'tsv', 'dsv'];\n/**\n * An array of file extensions that contain genomic sequence content.\n */\nexport const FILE_TXT_GENOMICS_EXTENSIONS = ['fasta', 'fna', 'fsa', 'fa', 'fastp', 'fastq', 'faa', 'gbk', 'gff', 'vcf', 'seq'];\n\n/**\n * An array of file extensions that are considered TXT files.\n */\nexport const FILE_TXT_EXTENSIONS = ['txt', 'log', 'yml', 'cfg', 'config', 'xml', 'yaml', ...FILE_DSV_EXTENSIONS, ...FILE_TXT_GENOMICS_EXTENSIONS];\n\n\n/**\n * An array of file extensions that are considered image files.\n */\nexport const FILE_IMAGE_EXTENSIONS = ['jpg', 'jpeg', 'png', 'svg'];\n\n/**\n * An array of file extensions that are considered OME (Open Microscopy Environment) files.\n */\nexport const FILE_OME_EXTENSIONS = ['tif', 'ome.tif', 'ome.tiff', 'ome.tif.gz', 'ome.tiff.gz'];\n\n/**\n * An array of file extensions that can be opened in the browser.\n * Includes common document formats such as HTML, PDF, and JSON, as well as image, DSV, TXT, and OME file formats.\n */\nexport const FILE_EXTENSIONS_TO_OPEN = ['html', 'pdf', 'json', 'fcs',\n    ...FILE_IMAGE_EXTENSIONS,\n    ...FILE_TXT_EXTENSIONS,\n    ...FILE_TRACK_EXTENSIONS,\n    ...FILE_PROTEIN_STRUCTURE_EXTENSIONS\n];\n\n\n/**\n * Checks if a file has an extension that matches one in the provided list.\n * @param filePath The file to check the extension of.\n * @param extensions A list of file endings to check the file against.\n * @returns True or false if the file has an ending in the extensions list.\n */\nexport function matchesExtension(filePath: string, extensions: string[]): boolean {\n    filePath = filePath.toLowerCase();\n\n    // Decompress the filePath if it ends with .gz\n    if (filePath.endsWith('.gz')) {\n        filePath = filePath.slice(0, -3);  // remove the .gz extension\n    }\n\n    // Now, get the extension of the file\n    const fileExtension = filePath.slice(filePath.lastIndexOf('.') + 1);\n\n    // Check if the fileExtension is in the list of extensions\n    return extensions.includes(fileExtension);\n}\n","import { AWSCredentials } from '@cirrobio/api-client';\n\nclass Mutex<T> {\n  private mutex = Promise.resolve();\n\n  lock(): PromiseLike<() => void> {\n    let begin: (unlock: () => void) => void = () => { /* Do nothing */ };\n\n    this.mutex = this.mutex.then(() => new Promise(begin));\n\n    return new Promise((res) => {\n      begin = res;\n    });\n  }\n\n  async dispatch(fn: (() => T) | (() => PromiseLike<T>)): Promise<T> {\n    const unlock = await this.lock();\n    try {\n      return await Promise.resolve(fn());\n    } finally {\n      unlock();\n    }\n  }\n}\n\n/**\n * A mutex to ensure that only one request for credentials is made at a time.\n */\nexport const credentialsMutex = new Mutex<AWSCredentials>();\n/**\n * A cache of credentials to avoid making multiple requests for the same credentials.\n */\nexport const credentialsCache: Map<string, AWSCredentials> = new Map<string, AWSCredentials>();\n","import { S3Client } from \"@aws-sdk/client-s3\";\nimport { AWSCredentials } from \"@cirrobio/api-client\";\n\nconst clientCache = new Map<string, S3Client>();\n\n/**\n * Creates an S3 client using the provided credentials.\n */\nexport function createS3Client(credentials: AWSCredentials): S3Client {\n  const cacheKey = `${credentials.accessKeyId}-${credentials.region}`;\n  const cachedClient = clientCache.get(cacheKey);\n  if (cachedClient) {\n    return cachedClient;\n  }\n  const newClient = new S3Client({\n    credentials: {\n      accessKeyId: credentials.accessKeyId,\n      secretAccessKey: credentials.secretAccessKey,\n      sessionToken: credentials.sessionToken,\n    },\n    region: credentials.region,\n    useDualstackEndpoint: true,\n  });\n  clientCache.set(cacheKey, newClient);\n  return newClient;\n}\n","/**\n * Converts an S3 URI to a bucket and key\n */\nexport function s3UriToParams(uri: string): { Bucket: string, Key: string } {\n  const matches = /^s3:\\/\\/([^/]+)\\/(.+)$/.exec(uri);\n  if (!matches) {\n    throw new Error(`Received invalid uri: '${uri}'`);\n  }\n  return {\n    Bucket: matches[1],\n    Key: matches[2],\n  };\n}\n\n","import { AWSCredentials } from \"@cirrobio/api-client\";\nimport { GetObjectCommand, GetObjectCommandInput } from \"@aws-sdk/client-s3\";\nimport { getSignedUrl as getSignedUrlInternal } from \"@aws-sdk/s3-request-presigner\";\nimport { createS3Client } from \"../util/s3-client\";\nimport { s3UriToParams } from \"../util/s3-utils\";\n\nexport interface GetFileUrlParams extends GetSignedUrlOptions {\n  url: string;\n  credentials?: AWSCredentials;\n}\n\nexport interface GetSignedUrlOptions {\n  download?: boolean;\n  gzip?: boolean;\n  timeout?: number;\n  filename?: string;\n}\n\n/**\n * Get a signed URL for a file in S3 given its S3 URI.\n * Defaults to a 5 minute timeout.\n */\nexport function getSignedUrl({ url, credentials, ...params }: GetFileUrlParams): Promise<string> {\n  const client = createS3Client(credentials);\n  const { Bucket, Key } = s3UriToParams(url);\n  const fileName = params.filename ?? Key.split('/').pop();\n  const args: GetObjectCommandInput = { Bucket, Key };\n  if (params?.download) {\n    args.ResponseContentDisposition = `attachment; filename=\"${fileName}\"`\n  }\n  if (params?.gzip) {\n    args.ResponseContentEncoding = 'gzip'\n  }\n  const command = new GetObjectCommand(args);\n  return getSignedUrlInternal(client, command, { expiresIn: 60 * (params?.timeout ?? 5) });\n}\n","\nconst resourcePrefix = 'project-';\n\nexport function getResourceName(projectId: string): string {\n  return `${resourcePrefix}${projectId}`;\n}\n\n","import { getResourceName } from \"../util/get-resource-name\";\n\n/**\n * Get the S3 bucket name for a project.\n * Will be deprecated in the future, use domain from manifest instead.\n */\nexport function getProjectS3Bucket(projectId: string): string {\n  return getResourceName(projectId)\n}\n","import { AWSCredentials, GenerateProjectFileAccessTokenRequest, ProjectAccessType } from \"@cirrobio/api-client\";\nimport { ProjectFileAccessContext } from \"./project-access-context\";\nimport { credentialsCache, credentialsMutex } from \"./util/credentials-mutex.so\";\nimport { GetFileUrlParams, getSignedUrl, GetSignedUrlOptions } from \"./actions/sign-url.fn\";\nimport { getProjectS3Bucket } from \"./shared\";\nimport { DownloadableFile } from \"./models/file-object.model\";\n\nexport interface IFileCredentialsApi {\n  generateProjectFileAccessToken: (params: GenerateProjectFileAccessTokenRequest) => Promise<AWSCredentials>;\n}\n\n/**\n * Service for viewing files in Cirro\n *  currently this only operates on files within a project\n */\nexport class FileService {\n  constructor(\n    private readonly fileCredsApi: IFileCredentialsApi\n  ) {}\n\n  /**\n   * Get contents of a file\n   */\n  async getProjectFile(file: DownloadableFile): Promise<Response> {\n    const url = await this.getSignedUrlFromProjectFile(file);\n    return fetch(url);\n  }\n\n  /**\n   * Get a signed URL for a file\n   */\n  async getSignedUrlFromProjectFile(file: DownloadableFile, params?: GetSignedUrlOptions): Promise<string> {\n    const credentials = await this.getProjectAccessCredentials(file.fileAccessContext);\n    const _params: GetFileUrlParams = {\n      ...params,\n      filename: file.name,\n      url: file.url,\n      credentials,\n    };\n    return getSignedUrl(_params);\n  }\n\n  /**\n   * Get a signed URL for a file given a path\n   */\n  async getSignedUrlFromProjectPath(fileAccessContext: ProjectFileAccessContext, path: string, params?: GetSignedUrlOptions): Promise<string> {\n    const credentials = await this.getProjectAccessCredentials(fileAccessContext);\n    const _params: GetFileUrlParams = {\n      ...params,\n      filename: path.split('/').pop(),\n      url: `s3://${getProjectS3Bucket(fileAccessContext.project.id)}/${path}`,\n      credentials,\n    };\n    return getSignedUrl(_params);\n  }\n\n  /**\n   * Get credentials for accessing a project file\n   */\n  async getProjectAccessCredentials(fileAccessContext: ProjectFileAccessContext): Promise<AWSCredentials> {\n    const accessType = fileAccessContext.fileAccessRequest.accessType;\n    // Special case for project download, since we can cache the credentials\n    if (accessType === ProjectAccessType.ProjectDownload || accessType === ProjectAccessType.SharedDatasetDownload) {\n      return this.getProjectReadCredentials(fileAccessContext);\n    }\n    return this.fileCredsApi.generateProjectFileAccessToken({ projectId: fileAccessContext.project.id, projectFileAccessRequest: fileAccessContext.fileAccessRequest });\n  }\n\n  private async getProjectReadCredentials(fileAccessContext: ProjectFileAccessContext): Promise<AWSCredentials> {\n    const projectId = fileAccessContext.project.id;\n    // Append datasetId to cache key for shared dataset downloads since we need to generate a new token for each dataset\n    let cacheKey = projectId;\n    if (fileAccessContext.fileAccessRequest.accessType === ProjectAccessType.SharedDatasetDownload) {\n      cacheKey = `${projectId}-${fileAccessContext.fileAccessRequest.datasetId}`;\n    }\n\n    return credentialsMutex.dispatch(async () => {\n      const cachedCredentials = credentialsCache.get(cacheKey);\n      const expirationTime = cachedCredentials ? cachedCredentials?.expiration : null;\n      const fetchNewCredentials = !expirationTime || expirationTime < new Date();\n      if (fetchNewCredentials) {\n        const projectFileAccessRequest = fileAccessContext.fileAccessRequest;\n        const credentials = await this.fileCredsApi.generateProjectFileAccessToken({ projectId, projectFileAccessRequest });\n        credentialsCache.set(cacheKey, credentials);\n        return credentials;\n      }\n      return cachedCredentials;\n    });\n  }\n}\n","import { AWSCredentials } from \"@cirrobio/api-client\";\nimport { DeleteObjectCommand } from \"@aws-sdk/client-s3\";\nimport { s3UriToParams } from \"../util/s3-utils\";\nimport { createS3Client } from \"../util/s3-client\";\n\nexport interface DeleteFileParams {\n  url: string;\n  credentials: AWSCredentials;\n}\n\n/**\n * Delete a file from S3 given its URL and credentials.\n */\nexport async function deleteFile({ url, credentials }: DeleteFileParams): Promise<void> {\n  const { Bucket, Key } = s3UriToParams(url);\n  const cmd = new DeleteObjectCommand({ Bucket, Key });\n  await createS3Client(credentials).send(cmd);\n}\n","import { Upload } from \"@aws-sdk/lib-storage\";\nimport { AWSCredentials } from '@cirrobio/api-client';\nimport { createS3Client } from \"../util/s3-client\";\nimport { PutObjectCommandInput } from \"@aws-sdk/client-s3\";\nimport { CreateMultipartUploadRequest } from \"@aws-sdk/client-s3/dist-types/models/models_0\";\n\nexport interface UploadFileParams {\n  bucket: string;\n  path: string;\n  file: File;\n  credentials: AWSCredentials;\n  metadata?: Record<string, string>;\n}\n\n/**\n * Upload a file to S3\n */\nexport function uploadFile({ bucket, path, file, credentials, metadata }: UploadFileParams): Upload {\n  const params: PutObjectCommandInput & CreateMultipartUploadRequest = {\n    Bucket: bucket,\n    Key: path,\n    Body: file,\n    ContentType: file.type,\n    Metadata: metadata,\n    ChecksumType: \"FULL_OBJECT\"\n  };\n  return new Upload({\n    client: createS3Client(credentials),\n    queueSize: 4,\n    params,\n  });\n}\n\n","import { ProjectAccessType, DatasetDetail, ProjectFileAccessRequest, Project } from \"@cirrobio/api-client\";\n\ntype ProjectIdentifiable = Pick<Project, 'id'>;\n\n/**\n * Helper class to encapsulate the file access for a project.\n */\nexport class ProjectFileAccessContext {\n  constructor(\n    readonly project: ProjectIdentifiable,\n    readonly dataset: DatasetDetail,\n    readonly fileAccessRequest: ProjectFileAccessRequest\n  ) {\n  }\n\n  static projectDownload(project: ProjectIdentifiable): ProjectFileAccessContext {\n    const request: ProjectFileAccessRequest = { accessType: ProjectAccessType.ProjectDownload };\n    return new ProjectFileAccessContext(project, null, request);\n  }\n\n  static datasetDownload(project: ProjectIdentifiable, dataset: DatasetDetail): ProjectFileAccessContext {\n    const accessType = dataset.share ? ProjectAccessType.SharedDatasetDownload : ProjectAccessType.ProjectDownload;\n    const request: ProjectFileAccessRequest = { accessType, datasetId: dataset.id };\n    return new ProjectFileAccessContext(project, dataset, request);\n  }\n}\n","import { ProjectFileAccessContext } from \"../project-access-context\";\n\nexport enum FileSystemObjectType {\n  FILE = 'file',\n  FOLDER = 'folder'\n}\n\n/**\n * Represents a file that can be downloaded\n */\nexport interface DownloadableFile {\n  url: string;\n  name?: string;\n  fileAccessContext: ProjectFileAccessContext;\n}\n\n/**\n * Represents a file in Cirro\n */\nexport interface FileSystemObject extends DownloadableFile {\n  /**\n   * Unique Id For Object\n   */\n  id: string;\n  /**\n   * Object S3 Url\n   */\n  url: string;\n  /**\n   * Object Path\n   */\n  path: string;\n  /**\n   * Object Name\n   */\n  name: string;\n  /**\n   * Object Size\n   */\n  size: number;\n  /**\n   * Object Kind (PNG, TXT)\n   */\n  kind: string;\n  /**\n   * Object Type (File or Folder)\n   */\n  type: FileSystemObjectType;\n  /**\n   * Metadata\n   */\n  metadata?: Record<string, any>;\n  /**\n   * Access context\n   */\n  fileAccessContext: ProjectFileAccessContext;\n}\n","import { FileSystemObject } from \"./models/file-object.model\";\n\n/**\n * Calculate the total size of all files in a directory.\n * @param files - An array of FileSystemObject representing the files in the directory.\n * @return The total size of all files in bytes.\n */\nexport function calculateTotalSize(files: Array<FileSystemObject>): number {\n  let totalSize = 0;\n  for (const file of files) {\n    totalSize += file.size;\n  }\n  return totalSize;\n}\n","/**\n * Pretty prints a JSON object with the specified indentation level.\n * @param obj JSON object to be pretty printed.\n * @param indentLevel Number of spaces to use for indentation.\n */\nexport function jsonPrettyPrint(obj: object, indentLevel=2): string {\n  return JSON.stringify(obj, null, indentLevel);\n}\n","/**\n * Format bytes as human-readable text.\n * @param bytes Number of bytes.\n * @param si True to use metric(SI) units, aka powers of 1000. False to use\n * binary(IEC), aka powers of 1024.\n   * @param dp Number of decimal places to display.\n *\n * @return Formatted string.\n */\nexport function bytesToString(bytes, si = false, dp = 1): string {\n  const thresh = si ? 1000 : 1024;\n\n  if (Math.abs(bytes) < thresh) {\n    return `${bytes} B`;\n  }\n\n  const units = si\n    ? ['kB', 'MB', 'GB', 'TB', 'PB', 'EB', 'ZB', 'YB']\n    : ['KiB', 'MiB', 'GiB', 'TiB', 'PiB', 'EiB', 'ZiB', 'YiB'];\n  let u = -1;\n  const r = 10 ** dp;\n\n  do {\n    bytes /= thresh;\n    ++u;\n  } while (\n    Math.round(Math.abs(bytes) * r) / r >= thresh\n    && u < units.length - 1\n    );\n\n  return `${bytes.toFixed(dp)} ${units[u]}`;\n}\n","/**\n * Normalizes a date to UTC by adjusting for the timezone offset.\n * Useful when you are working with dates that may not include time information.\n * @param date\n */\nexport function normalizeDate(date: Date | string | undefined | null): Date {\n  if (!date) throw new Error(\"Attempt to normalize undefined\");\n  if (!(date instanceof Date)) date = new Date(date);\n  return new Date(date.getTime() - date.getTimezoneOffset() * -60000);\n}\n","/**\n * Normalize a string by trimming it and returning null if it is empty.\n * @param input The string to normalize.\n */\nexport function normalizeString(input: string): string {\n  if (!input?.trim()) return null;\n  return input.trim();\n}\n","/**\n * Removes the starting slash from a path.\n * @param path Input path\n */\nexport function removeStartingSlash(path: string): string {\n  if (!path) return path;\n  if (path.startsWith('./')) return path.substring(2);\n  if (path.startsWith('/')) return path.substring(1);\n  return path;\n}\n\n/**\n * Removes the ending slash from a path.\n * @param path Input path\n */\nexport function removeEndingSlash(path: string): string {\n  return path?.endsWith('/') ? path.slice(0, -1) : path;\n}\n","const dateFormat = new Intl.DateTimeFormat('en-US', { month: '2-digit', day: '2-digit', year: '2-digit' });\n\n/**\n * Converts a date string or Date object to MM/DD/YY date string.\n * Ex., \"2023-10-01\" -> \"10/01/23\"\n * @param date Input date string or Date object.\n */\nexport function toDateFormat(date: string | Date): string {\n  if (!date) return null;\n  const d: Date = (typeof date === 'string') ? new Date(date) : date\n  return dateFormat.format(d);\n}\n","/**\n * Converts a string to Title case.\n * Ex., \"hello world\" -> \"Hello world\"\n * @param value\n */\nexport function toTitleCase(value: string): string {\n  if (!value) return null;\n  return value[0].toUpperCase() + value.slice(1).toLowerCase();\n}\n","import { toTitleCase } from './to-title-case';\n\n/**\n * Converts a field name to a more human-readable format.\n * Ex., \"helloWorld\" -> \"Hello World\"\n * @param value The value to convert.\n */\nexport function toFriendlyName(value: string): string {\n  let _value = value.split(/(?=[A-Z])/).join(' ');\n  _value = _value.split('_').join(' ');\n  _value = _value.split('|').join(' ');\n  _value = _value.replace(/ +/g, ' ');\n  return toTitleCase(_value);\n}\n","const money = new Intl.NumberFormat('en-US', {\n  style: 'currency',\n  currency: 'USD',\n});\n\n/**\n * Converts a number or bigint to a formatted money string.\n * Ex., 1234.56 -> $1,234.56\n * @param value Input number or bigint value.\n */\nexport function toMoney(value: number | bigint): string {\n  return money.format(value as number);\n}\n","/**\n * Converts a string to PascalCase.\n * Ex., \"hello world\" -> \"HelloWorld\"\n * @param value The string to convert.\n */\nexport function toPascalCase(value: string): string {\n  return value.replace(/(\\w)(\\w*)/g, (g0, g1, g2) => g1.toUpperCase() + g2.toLowerCase());\n}\n","import { calculateTotalSize } from \"../calculate-size\";\nimport { bytesToString } from \"../../formatters\";\nimport { FileSystemObject } from \"./file-object.model\";\n\nexport class Assets extends Array<FileSystemObject> {\n  private _totalSize: string;\n  private _totalSizeBytes: number;\n\n  // Total size of all files in human-readable format\n  get totalSize(): string {\n    if (!this._totalSize) {\n      this.calculateSize();\n    }\n    return this._totalSize;\n  }\n\n  get totalSizeBytes(): number {\n    if (!this._totalSizeBytes) {\n      this.calculateSize();\n    }\n    return this._totalSizeBytes;\n  }\n  private calculateSize(): void {\n    this._totalSizeBytes = calculateTotalSize(this);\n    this._totalSize = bytesToString(this._totalSizeBytes)\n  }\n}\n","import { v4 as uuidv4 } from 'uuid';\nimport { FileSystemObject, FileSystemObjectType } from \"./file-object.model\";\n\nexport class Folder implements FileSystemObject {\n  readonly id: string;\n  readonly url: string;\n  readonly path: string;\n  readonly name: string;\n  readonly domain: string;\n  readonly kind = 'Folder';\n  readonly fileAccessContext = null;\n  readonly size = 0;\n  readonly type = FileSystemObjectType.FOLDER;\n\n  constructor(url: string, name: string, path: string, domain: string) {\n    this.id = uuidv4();\n    this.url = url;\n    this.name = name;\n    this.path = path;\n    this.domain = domain;\n  }\n}\n","import { FileSystemObject, FileSystemObjectType } from \"./file-object.model\";\nimport { ProjectFileAccessContext } from \"../project-access-context\";\nimport { v4 as uuidv4 } from 'uuid';\n\nexport class File implements FileSystemObject {\n  readonly id: string;\n  readonly url: string\n  readonly size: number;\n  readonly path: string;\n  readonly name: string;\n  readonly metadata: Record<string, any>;\n  readonly fileAccessContext: ProjectFileAccessContext;\n\n  get type() {\n    return FileSystemObjectType.FILE;\n  }\n\n  get kind() {\n    return this.path.slice(this.\n    path.lastIndexOf('.') + 1);\n  }\n\n  constructor(domain: string, file: string, size: number, metadata: Record<string, any>, accessContext: ProjectFileAccessContext) {\n    this.id = uuidv4();\n    this.url = `${domain}/${file}`;\n    this.size = size;\n    this.metadata = metadata;\n    this.fileAccessContext = accessContext;\n\n    const fileFolderIdx = file.lastIndexOf('/');\n    if (fileFolderIdx === -1) {\n      this.path = '';\n      this.name = file;\n    } else {\n      this.path = file.substring(0, fileFolderIdx);\n      this.name = file.substring(fileFolderIdx + 1);\n    }\n  }\n}\n","import { DatasetAssetsManifest, FileEntry } from '@cirrobio/api-client';\nimport { Assets } from \"./models/assets\";\nimport { Folder } from \"./models/folder\";\nimport { File } from \"./models/file\";\nimport { ProjectFileAccessContext } from \"./project-access-context\";\nimport { removeEndingSlash } from \"../formatters\";\n\n\nexport class ManifestParser {\n  private readonly manifest: DatasetAssetsManifest;\n  private readonly accessContext: ProjectFileAccessContext;\n\n  constructor(manifest: DatasetAssetsManifest, accessContext?: ProjectFileAccessContext) {\n    this.manifest = manifest;\n    this.accessContext = accessContext;\n  }\n\n  private get files(): Array<FileEntry> {\n    return this.manifest?.files ?? [];\n  }\n\n  /**\n   * Generates asset objects from the manifest, optionally including folder entries.\n   */\n  public generateAssets(generateFolders = false): Assets {\n    const domain = removeEndingSlash(this.manifest?.domain);\n    const assets = new Assets();\n\n    for (const file of this.files) {\n      assets.push(new File(domain, file.path, file.size, file.metadata, this.accessContext));\n    }\n\n    // Optionally add folder entries\n    if (generateFolders) {\n      assets.push(...this.generateFolderAssets(assets, domain));\n    }\n\n    return assets;\n  }\n\n  // Create folder entries, useful for visualizing folders as items in a file browser\n  private generateFolderAssets(assets: Assets, domain: string): Folder[] {\n    const folderSet = new Set<string>();\n\n    // Collect all unique folder paths\n    for (const asset of assets) {\n      const parts = asset.path.split('/').filter(p => p.length > 0);\n      let currentPath = '';\n      for (const part of parts) {\n        currentPath = currentPath ? `${currentPath}/${part}` : part;\n        folderSet.add(currentPath);\n      }\n    }\n\n    // Create Folder objects from unique paths\n    return Array.from(folderSet)\n      .map(folderPath => {\n        const name = folderPath.substring(folderPath.lastIndexOf('/') + 1);\n        const parentPath = folderPath.includes('/') ? folderPath.substring(0, folderPath.lastIndexOf('/')) : '';\n        return new Folder(folderPath, name, parentPath, domain);\n      });\n  }\n}\n","\n/**\n * Returns the parent directory of a given file path.\n */\nexport function getParentPath(path: string): string {\n  return path.split(\"/\").slice(0, -1).join(\"/\") ?? \"\"\n}\n","export class ApiError extends Error {\n  errors: string[];\n\n  constructor(message: string, errors: string[]) {\n    super(message);\n    this.errors = errors;\n  }\n}\n","import { Middleware, ResponseContext } from \"@cirrobio/api-client\";\nimport { ApiError } from \"./error\";\n\nexport class PortalErrorHandler implements Middleware {\n  async post(context: ResponseContext): Promise<Response | void> {\n    const { response } = context;\n    if (response && (response.status >= 200 && response.status < 300)) {\n      return response;\n    }\n\n    // Handle Error\n    let errorMessage: string;\n    const errors = [];\n    try {\n      const err = await response.json();\n      console.warn(err);\n      if ('errorDetail' in err) {\n        errorMessage = err.errorDetail;\n        errors.push(err.errors.map((e: any) => e.message));\n      } else {\n        errorMessage = err.message;\n      }\n    } catch (ignore) {\n      errorMessage = \"Unknown Error\";\n    }\n    throw new ApiError(errorMessage, errors);\n  }\n}\n","import { PortalErrorHandler } from \"./error-handler\";\nimport { Configuration } from \"@cirrobio/api-client\";\n\ninterface GetConfigParams {\n  tokenGetter: () => Promise<string>;\n  basePath?: string;\n}\n\nexport const generateApiConfig = ({ basePath = \"/api\", tokenGetter}: GetConfigParams) => {\n  return new Configuration({\n    basePath,\n    accessToken: tokenGetter,\n    middleware: [\n      new PortalErrorHandler()\n    ],\n  });\n}\n","export class CurrentUser {\n  username: string;\n  /**\n   * The unique identifier for the user\n   */\n  sub: string\n\n  /**\n   * The time the user authenticated\n   */\n  authTime: Date;\n\n  /**\n   * The groups the user belongs to\n   */\n  groups: string[];\n\n  static fromCognitoUser(idTokenPayload: Record<string, any>): CurrentUser {\n    return {\n      username: idTokenPayload[\"cognito:username\"] ?? idTokenPayload.username,\n      sub: idTokenPayload.sub,\n      authTime: new Date(idTokenPayload.auth_time * 1000),\n      groups: idTokenPayload[\"cognito:groups\"] ?? [],\n    };\n  }\n}\n","import { SystemInfoResponse } from \"@cirrobio/api-client\";\nimport { AuthenticationProvider } from \"./authentication-provider\";\nimport { CurrentUser } from \"./current-user\";\n\n\nexport class StaticTokenAuthProvider implements AuthenticationProvider {\n  constructor(\n    readonly token: string\n  ) {\n  }\n\n  public configure(_ignore: SystemInfoResponse): void {\n    console.log('StaticTokenAuthProvider loaded');\n  }\n\n  public async getAccessToken() {\n    return this.token;\n  }\n\n  public async getCurrentUser() {\n    const accessToken = await this.getAccessToken();\n    const parsedToken = JSON.parse(atob(accessToken.split('.')[1]));\n    return CurrentUser.fromCognitoUser(parsedToken);\n  }\n\n  public forceRefresh(): Promise<void> {\n    return Promise.resolve();\n  }\n}\n","import {\n  AuditApi,\n  BillingApi,\n  ComputeEnvironmentApi,\n  Configuration,\n  DatasetsApi,\n  ExecutionApi,\n  FileApi,\n  GovernanceApi,\n  MetadataApi,\n  NotebooksApi,\n  ProcessesApi,\n  ProjectRequestsApi,\n  ProjectsApi,\n  ReferencesApi,\n  SharingApi,\n  SystemApi,\n  ToolsApi,\n  UsersApi\n} from \"@cirrobio/api-client\";\nimport { generateApiConfig } from \"../api/config\";\n\ninterface DataServiceParams {\n  tokenGetter: () => Promise<string>;\n  basePath?: string;\n}\n\nexport class DataService {\n  private readonly apiConfig: Configuration;\n\n  private readonly _auditApi: AuditApi;\n  private readonly _billingApi: BillingApi;\n  private readonly _computeEnvironmentApi: ComputeEnvironmentApi;\n  private readonly _datasetsApi: DatasetsApi;\n  private readonly _executionApi: ExecutionApi;\n  private readonly _fileApi: FileApi;\n  private readonly _governanceApi: GovernanceApi;\n  private readonly _metadataApi: MetadataApi;\n  private readonly _notebooksApi: NotebooksApi;\n  private readonly _processesApi: ProcessesApi;\n  private readonly _projectRequestsApi: ProjectRequestsApi;\n  private readonly _projectsApi: ProjectsApi;\n  private readonly _referencesApi: ReferencesApi;\n  private readonly _sharingApi: SharingApi;\n  private readonly _systemApi: SystemApi;\n  private readonly _toolsApi: ToolsApi;\n  private readonly _usersApi: UsersApi;\n\n  constructor({ tokenGetter, basePath = \"/api\" }: DataServiceParams) {\n    this.apiConfig = generateApiConfig({ basePath, tokenGetter });\n\n    this._auditApi = new AuditApi(this.apiConfig);\n    this._billingApi = new BillingApi(this.apiConfig);\n    this._computeEnvironmentApi = new ComputeEnvironmentApi(this.apiConfig);\n    this._datasetsApi = new DatasetsApi(this.apiConfig);\n    this._executionApi = new ExecutionApi(this.apiConfig);\n    this._fileApi = new FileApi(this.apiConfig);\n    this._governanceApi = new GovernanceApi(this.apiConfig);\n    this._metadataApi = new MetadataApi(this.apiConfig);\n    this._notebooksApi = new NotebooksApi(this.apiConfig);\n    this._processesApi = new ProcessesApi(this.apiConfig);\n    this._projectRequestsApi = new ProjectRequestsApi(this.apiConfig);\n    this._projectsApi = new ProjectsApi(this.apiConfig);\n    this._referencesApi = new ReferencesApi(this.apiConfig);\n    this._sharingApi = new SharingApi(this.apiConfig);\n    this._systemApi = new SystemApi(this.apiConfig);\n    this._toolsApi = new ToolsApi(this.apiConfig);\n    this._usersApi = new UsersApi(this.apiConfig);\n  }\n\n  get audit(): AuditApi {\n    return this._auditApi;\n  }\n  get billing(): BillingApi {\n    return this._billingApi;\n  }\n  get computeEnvironments(): ComputeEnvironmentApi {\n    return this._computeEnvironmentApi;\n  }\n  get datasets(): DatasetsApi {\n    return this._datasetsApi;\n  }\n  get execution(): ExecutionApi {\n    return this._executionApi;\n  }\n  get file(): FileApi {\n    return this._fileApi;\n  }\n  get governance(): GovernanceApi {\n    return this._governanceApi;\n  }\n  get metadata(): MetadataApi {\n    return this._metadataApi;\n  }\n  get notebooks(): NotebooksApi {\n    return this._notebooksApi;\n  }\n  get processes(): ProcessesApi {\n    return this._processesApi;\n  }\n  get projectRequests(): ProjectRequestsApi {\n    return this._projectRequestsApi;\n  }\n  get projects(): ProjectsApi {\n    return this._projectsApi;\n  }\n  get references(): ReferencesApi {\n    return this._referencesApi;\n  }\n  get sharing(): SharingApi {\n    return this._sharingApi;\n  }\n  get system(): SystemApi {\n    return this._systemApi;\n  }\n  get tools(): ToolsApi {\n    return this._toolsApi;\n  }\n  get users(): UsersApi {\n    return this._usersApi;\n  }\n}\n","/**\n * Extracts a value from an object using the json path notation, i.e. $.test.id\n * @param path JSON path to the value\n * @param obj Object to extract the value from\n */\nexport function extractFromObject(path: string, obj: object): any {\n  const pathParts = path.slice(2).split('.')\n  return pathParts.reduce(function(o, k) {\n    return o && o[k];\n  }, obj);\n}\n","/**\n * Ignores dangling promise 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package/dist/types/api/config.d.ts

@@ -1,7 +1,6 @@
-import { Configuration } from "@cirrobio/api-client";
 interface GetConfigParams {
     tokenGetter: () => Promise<string>;
     basePath?: string;
 }
-export declare const generateApiConfig: ({ basePath, tokenGetter }: GetConfigParams) => Configuration;
+export declare const generateApiConfig: ({ basePath, tokenGetter }: GetConfigParams) => any;
 export {};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cirrobio/sdk",
-  "version": "0.10.5",
+  "version": "0.10.6",
   "description": "SDK for Cirro",
   "author": "CirroBio",
   "repository": {
@@ -30,10 +30,10 @@
     "preset": "ts-jest"
   },
   "dependencies": {
-    "@aws-sdk/client-s3": "^3.34.0",
-    "@aws-sdk/lib-storage": "^3.34.0",
-    "@aws-sdk/s3-request-presigner": "^3.34.0",
-    "@cirrobio/api-client": "^0.10.1",
+    "@aws-sdk/client-s3": "^3.886.0",
+    "@aws-sdk/lib-storage": "^3.886.0",
+    "@aws-sdk/s3-request-presigner": "^3.886.0",
+    "@cirrobio/api-client": "^0.10.2",
     "uuid": "^11.1.0"
   },
   "devDependencies": {