@fnndsc/cumin 3.2.4

package/dist/io/chrisIO.d.ts

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+/**
+ * @file ChRIS IO Operations
+ *
+ * This module handles file input/output operations with the ChRIS backend,
+ * including downloading and uploading files.
+ *
+ * @module
+ */
+import Client from "@fnndsc/chrisapi";
+import { IStorageProvider } from "./io.js";
+import { Result } from "../utils/result.js";
+/**
+ * Class for handling IO operations with ChRIS.
+ */
+export declare class ChrisIO {
+    private _chrisFolder;
+    private _client;
+    private storageProvider;
+    constructor();
+    /**
+     * Sets the storage provider for local IO operations.
+     * @param provider - The storage provider instance.
+     */
+    storageProvider_set(provider: IStorageProvider): void;
+    /**
+     * Gets the ChRIS client instance, initializing it if necessary.
+     * @returns A Promise resolving to the Client instance or null.
+     */
+    client_get(): Promise<Client | null>;
+    get chrisFolder(): string;
+    set chrisFolder(folder: string);
+    /**
+     * Initializes the ChrisIO instance by creating a file browser folder.
+     * @returns A Promise resolving to true on success, false on failure, or null if client is missing.
+     */
+    init(): Promise<boolean | null>;
+    private isArrayBuffer;
+    /**
+     * Downloads a file from ChRIS by its ID as a stream (Node) or blob (browser).
+     * Returns the raw response data plus optional size metadata when available.
+     *
+     * @param fileId - The ID of the file to download.
+     * @returns A Result containing the stream/blob and optional size metadata.
+     */
+    file_downloadStream(fileId: number): Promise<Result<{
+        stream: unknown;
+        size?: number;
+        filename?: string;
+    }>>;
+    /**
+     * Downloads a file from ChRIS by its ID.
+     * @param fileId - The ID of the file to download.
+     * @returns A Promise resolving to a Buffer of the file content, or null on failure.
+     */
+    file_download(fileId: number): Promise<Buffer | null>;
+    /**
+     * Uploads a file to ChRIS.
+     * @param fileBlob - The file content as a Blob.
+     * @param uploadDir - The directory path in ChRIS to upload to.
+     * @param filename - The name of the file to create.
+     * @returns A Promise resolving to true on success, false on failure.
+     */
+    file_upload(fileBlob: Blob, uploadDir: string, filename: string): Promise<boolean>;
+    /**
+     * Creates a new folder in ChRIS at the specified path.
+     *
+     * @param folderPath - The path where the folder should be created.
+     * @returns A Result containing true if created, false if already exists, or Err on error.
+     *
+     * @example
+     * ```typescript
+     * const result = await chrisIO.folder_create('/uploads/data');
+     * if (result.ok && result.value) {
+     *   console.log('Folder created successfully');
+     * }
+     * ```
+     */
+    folder_create(folderPath: string): Promise<Result<boolean>>;
+    /**
+     * Moves (renames) a folder in ChRIS by updating its path.
+     * @param srcPath - The current folder path.
+     * @param destPath - The new folder path.
+     * @returns Promise resolving to true on success, false on failure.
+     */
+    folder_moveByPath(srcPath: string, destPath: string): Promise<Result<boolean>>;
+    /**
+     * Moves (renames) a file in ChRIS by updating its path.
+     * @param fileId - The file ID.
+     * @param destPath - The target path including filename.
+     * @returns Promise resolving to true on success, false on failure.
+     */
+    file_moveById(fileId: number, destPath: string): Promise<Result<boolean>>;
+    /**
+     * Uploads a local directory or file to ChRIS recursively.
+     * @param localPath - The path on the local filesystem.
+     * @param remotePath - The destination path on ChRIS. For directories, follows Unix cp semantics:
+     *                     the source directory name is appended to remotePath.
+     * @returns Promise<boolean> success status.
+     */
+    uploadLocalPath(localPath: string, remotePath: string): Promise<boolean>;
+    /**
+     * Performs a dummy upload for testing purposes.
+     * @returns A Promise resolving to true on success, or null if client is missing.
+     */
+    dummy_upload(): Promise<boolean | null>;
+}
+/**
+ * Global ChRIS IO instance.
+ */
+export declare const chrisIO: ChrisIO;

package/dist/io/chrisIO.js

@@ -0,0 +1,415 @@
+"use strict";
+/**
+ * @file ChRIS IO Operations
+ *
+ * This module handles file input/output operations with the ChRIS backend,
+ * including downloading and uploading files.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.chrisIO = exports.ChrisIO = void 0;
+const chrisConnection_js_1 = require("../connect/chrisConnection.js");
+const errorStack_js_1 = require("../error/errorStack.js");
+const result_js_1 = require("../utils/result.js");
+/**
+ * Class for handling IO operations with ChRIS.
+ */
+class ChrisIO {
+    constructor() {
+        this._chrisFolder = "";
+        this._client = null;
+        this.storageProvider = null;
+        // Client initialization is deferred or handled via async accessor
+    }
+    /**
+     * Sets the storage provider for local IO operations.
+     * @param provider - The storage provider instance.
+     */
+    storageProvider_set(provider) {
+        this.storageProvider = provider;
+    }
+    /**
+     * Gets the ChRIS client instance, initializing it if necessary.
+     * @returns A Promise resolving to the Client instance or null.
+     */
+    async client_get() {
+        if (!this._client) {
+            this._client = await chrisConnection_js_1.chrisConnection.client_get();
+        }
+        return this._client;
+    }
+    get chrisFolder() {
+        return this._chrisFolder;
+    }
+    set chrisFolder(folder) {
+        this._chrisFolder = folder;
+    }
+    /**
+     * Initializes the ChrisIO instance by creating a file browser folder.
+     * @returns A Promise resolving to true on success, false on failure, or null if client is missing.
+     */
+    async init() {
+        const client = await this.client_get();
+        if (!client) {
+            return null;
+        }
+        try {
+            const fileBrowserFolder = await client.createFileBrowserFolder({ path: this.chrisFolder });
+            return true;
+        }
+        catch (error) {
+            errorStack_js_1.errorStack.stack_push("error", `Failed to create FileBrowserFolder: 
+        ${error instanceof Error ? error.message : String(error)}`);
+            return false;
+        }
+    }
+    isArrayBuffer(obj) {
+        return (obj instanceof ArrayBuffer ||
+            (typeof obj === "object" && obj !== null && "byteLength" in obj));
+    }
+    /**
+     * Downloads a file from ChRIS by its ID as a stream (Node) or blob (browser).
+     * Returns the raw response data plus optional size metadata when available.
+     *
+     * @param fileId - The ID of the file to download.
+     * @returns A Result containing the stream/blob and optional size metadata.
+     */
+    async file_downloadStream(fileId) {
+        const client = await this.client_get();
+        if (!client) {
+            errorStack_js_1.errorStack.stack_push("error", "ChRIS client is not initialized");
+            return (0, result_js_1.Err)();
+        }
+        try {
+            const userFile = await client.getUserFile(fileId);
+            if (!userFile) {
+                errorStack_js_1.errorStack.stack_push("error", `File ID ${fileId} not found (404) or access denied (403).`);
+                return (0, result_js_1.Err)();
+            }
+            const response = await userFile.getFileStream();
+            if (!response || response.data === undefined) {
+                errorStack_js_1.errorStack.stack_push("error", `File ID ${fileId} returned no data.`);
+                return (0, result_js_1.Err)();
+            }
+            const lengthHeader = response.headers?.["content-length"] ||
+                response.headers?.["Content-Length"];
+            const size = typeof lengthHeader === "string" ? parseInt(lengthHeader, 10) : undefined;
+            return (0, result_js_1.Ok)({
+                stream: response.data,
+                size: Number.isFinite(size) ? size : undefined,
+                filename: userFile.data?.fname,
+            });
+        }
+        catch (error) {
+            const msg = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push("error", `Download stream failed for file ${fileId}: ${msg}`);
+            return (0, result_js_1.Err)();
+        }
+    }
+    /**
+     * Downloads a file from ChRIS by its ID.
+     * @param fileId - The ID of the file to download.
+     * @returns A Promise resolving to a Buffer of the file content, or null on failure.
+     */
+    async file_download(fileId) {
+        const client = await this.client_get();
+        if (!client) {
+            errorStack_js_1.errorStack.stack_push("error", "ChRIS client is not initialized");
+            return null;
+        }
+        try {
+            const userFile = await client.getUserFile(fileId);
+            if (!userFile) {
+                // This is a common case: the file ID was scraped from a listing, but
+                // the file itself is not retrievable (e.g. 404, or permissions)
+                errorStack_js_1.errorStack.stack_push("error", `File ID ${fileId} not found (404) or access denied (403).`);
+                return null;
+            }
+            const blob = await userFile.getFileBlob();
+            if (!blob) {
+                errorStack_js_1.errorStack.stack_push("error", `File ID ${fileId} exists but returned no content/blob.`);
+                return null;
+            }
+            if (typeof blob === "string") {
+                return Buffer.from(blob);
+            }
+            else if (Buffer.isBuffer(blob)) {
+                // Already a Node.js Buffer
+                return blob;
+            }
+            else if (blob instanceof ArrayBuffer) {
+                return Buffer.from(blob);
+            }
+            else if (blob instanceof Blob) {
+                const arrayBuffer = await blob.arrayBuffer();
+                return Buffer.from(arrayBuffer);
+            }
+            else {
+                throw new Error(`Unexpected blob type: ${typeof blob}`);
+            }
+        }
+        catch (error) {
+            // Catch network errors, timeouts, or specific API error messages
+            const msg = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push("error", `Download failed for file ${fileId}: ${msg}`);
+            return null;
+        }
+    }
+    /**
+     * Uploads a file to ChRIS.
+     * @param fileBlob - The file content as a Blob.
+     * @param uploadDir - The directory path in ChRIS to upload to.
+     * @param filename - The name of the file to create.
+     * @returns A Promise resolving to true on success, false on failure.
+     */
+    async file_upload(fileBlob, uploadDir, filename) {
+        const client = await this.client_get();
+        if (!client) {
+            console.error("ChRIS client is not initialized");
+            return false;
+        }
+        try {
+            // ChRIS API expects paths WITHOUT leading slash
+            // upload_path should be the FULL PATH including filename
+            const normalizedUploadDir = uploadDir.startsWith('/') ? uploadDir.substring(1) : uploadDir;
+            const fullPath = normalizedUploadDir.endsWith('/')
+                ? normalizedUploadDir + filename
+                : normalizedUploadDir + '/' + filename;
+            const data = {
+                upload_path: fullPath,
+            };
+            let fileObj = fileBlob;
+            if (typeof File !== 'undefined') {
+                fileObj = new File([fileBlob], filename);
+            }
+            const uploadFileObj = { fname: fileObj };
+            const uploadPromise = client.uploadFile(data, uploadFileObj);
+            const timeoutPromise = new Promise((_, reject) => setTimeout(() => reject(new Error('Upload timeout after 30s')), 30000));
+            const userFile = await Promise.race([uploadPromise, timeoutPromise]);
+            // ChRIS may rename the file to avoid collisions (e.g. world.txt → world_XXXXXXX.txt)
+            // when the path was recently deleted and not yet committed. Detect and rename back.
+            const actualFname = userFile.data?.fname ?? '';
+            const normalizedActual = actualFname.startsWith('/') ? actualFname.substring(1) : actualFname;
+            if (normalizedActual && normalizedActual !== fullPath) {
+                try {
+                    await userFile.put({ upload_path: fullPath });
+                }
+                catch (renameErr) {
+                    const renameMsg = renameErr instanceof Error ? renameErr.message : String(renameErr);
+                    errorStack_js_1.errorStack.stack_push('warning', `Uploaded as '${actualFname}' — rename to '${fullPath}' failed: ${renameMsg}`);
+                    // Don't fail the upload — file was uploaded, just at wrong name
+                }
+            }
+            return true;
+        }
+        catch (error) {
+            const errorMsg = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push("error", `Failed to upload file ${filename} to ${uploadDir}: ${errorMsg}`);
+            return false;
+        }
+    }
+    /**
+     * Creates a new folder in ChRIS at the specified path.
+     *
+     * @param folderPath - The path where the folder should be created.
+     * @returns A Result containing true if created, false if already exists, or Err on error.
+     *
+     * @example
+     * ```typescript
+     * const result = await chrisIO.folder_create('/uploads/data');
+     * if (result.ok && result.value) {
+     *   console.log('Folder created successfully');
+     * }
+     * ```
+     */
+    async folder_create(folderPath) {
+        const client = await this.client_get();
+        if (!client) {
+            errorStack_js_1.errorStack.stack_push("error", "ChRIS client is not initialized");
+            return (0, result_js_1.Err)();
+        }
+        try {
+            const folderList = await client.getFileBrowserFolders();
+            const response = await folderList.post({ path: folderPath });
+            if (response && response.data) {
+                return (0, result_js_1.Ok)(true); // Folder created successfully
+            }
+            else {
+                errorStack_js_1.errorStack.stack_push("error", `Failed to create folder: ${folderPath}. No data in response.`);
+                return (0, result_js_1.Err)();
+            }
+        }
+        catch (error) {
+            // Check if this is an "already exists" error (400 status with specific message)
+            if (error &&
+                typeof error === 'object' &&
+                'response' in error &&
+                error.response &&
+                typeof error.response === 'object' &&
+                'status' in error.response &&
+                error.response.status === 400 &&
+                'data' in error.response &&
+                error.response.data &&
+                typeof error.response.data === 'object' &&
+                'path' in error.response.data &&
+                Array.isArray(error.response.data.path) &&
+                error.response.data.path[0] &&
+                typeof error.response.data.path[0] === 'string' &&
+                error.response.data.path[0].includes('already exists')) {
+                errorStack_js_1.errorStack.stack_push("warning", `Folder '${folderPath}' already exists.`);
+                return (0, result_js_1.Ok)(false); // Return false to indicate folder already existed
+            }
+            // Other errors
+            const errorMessage = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push("error", `Error creating folder '${folderPath}': ${errorMessage}`);
+            return (0, result_js_1.Err)();
+        }
+    }
+    /**
+     * Moves (renames) a folder in ChRIS by updating its path.
+     * @param srcPath - The current folder path.
+     * @param destPath - The new folder path.
+     * @returns Promise resolving to true on success, false on failure.
+     */
+    async folder_moveByPath(srcPath, destPath) {
+        const client = await this.client_get();
+        if (!client) {
+            errorStack_js_1.errorStack.stack_push("error", "ChRIS client is not initialized");
+            return (0, result_js_1.Err)();
+        }
+        try {
+            const folder = await client.getFileBrowserFolderByPath(srcPath);
+            if (!folder) {
+                errorStack_js_1.errorStack.stack_push("error", `Folder not found: ${srcPath}`);
+                return (0, result_js_1.Err)();
+            }
+            // chrisapi typings omit the path field, but API supports it for renames
+            await folder.put({ path: destPath });
+            return (0, result_js_1.Ok)(true);
+        }
+        catch (error) {
+            const errorMsg = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push("error", `Failed to move folder ${srcPath} to ${destPath}: ${errorMsg}`);
+            return (0, result_js_1.Err)();
+        }
+    }
+    /**
+     * Moves (renames) a file in ChRIS by updating its path.
+     * @param fileId - The file ID.
+     * @param destPath - The target path including filename.
+     * @returns Promise resolving to true on success, false on failure.
+     */
+    async file_moveById(fileId, destPath) {
+        const client = await this.client_get();
+        if (!client) {
+            errorStack_js_1.errorStack.stack_push("error", "ChRIS client is not initialized");
+            return (0, result_js_1.Err)();
+        }
+        try {
+            const userFile = await client.getUserFile(fileId);
+            if (!userFile) {
+                errorStack_js_1.errorStack.stack_push("error", `File not found with ID ${fileId}`);
+                return (0, result_js_1.Err)();
+            }
+            // chrisapi typings omit the path field, but API supports it for renames
+            await userFile.put({ path: destPath });
+            return (0, result_js_1.Ok)(true);
+        }
+        catch (error) {
+            const errorMsg = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push("error", `Failed to move file ID ${fileId} to ${destPath}: ${errorMsg}`);
+            return (0, result_js_1.Err)();
+        }
+    }
+    /**
+     * Uploads a local directory or file to ChRIS recursively.
+     * @param localPath - The path on the local filesystem.
+     * @param remotePath - The destination path on ChRIS. For directories, follows Unix cp semantics:
+     *                     the source directory name is appended to remotePath.
+     * @returns Promise<boolean> success status.
+     */
+    async uploadLocalPath(localPath, remotePath) {
+        if (!this.storageProvider) {
+            errorStack_js_1.errorStack.stack_push("error", "Storage provider not configured in ChrisIO.");
+            return false;
+        }
+        try {
+            const isDir = await this.storageProvider.isDirectory(localPath);
+            if (isDir) {
+                // For directories, follow Unix cp semantics: append source dir basename to target
+                // e.g., upload ~/test-upload /home/user -> /home/user/test-upload/
+                const dirBasename = this.storageProvider.basename(localPath);
+                const targetDir = remotePath.endsWith('/')
+                    ? remotePath + dirBasename
+                    : remotePath + '/' + dirBasename;
+                const entries = await this.storageProvider.readdir(localPath);
+                let success = true;
+                for (const entry of entries) {
+                    const childLocal = this.storageProvider.join(localPath, entry);
+                    const childRemote = targetDir.endsWith('/')
+                        ? targetDir + entry
+                        : targetDir + '/' + entry;
+                    const result = await this.uploadLocalPath(childLocal, childRemote);
+                    if (!result)
+                        success = false;
+                }
+                return success;
+            }
+            else {
+                // It's a file
+                const content = await this.storageProvider.readBinary(localPath);
+                if (!content) {
+                    errorStack_js_1.errorStack.stack_push("error", `Failed to read local file: ${localPath}`);
+                    return false;
+                }
+                const blob = new Blob([content]);
+                // Split remotePath into dir and filename
+                // Since remote path is ChRIS path (Unix-like), we split by last '/'
+                const lastSlashIndex = remotePath.lastIndexOf('/');
+                let dir = "";
+                let name = remotePath;
+                if (lastSlashIndex !== -1) {
+                    dir = remotePath.substring(0, lastSlashIndex);
+                    name = remotePath.substring(lastSlashIndex + 1);
+                }
+                // If dir is empty, use root
+                if (!dir)
+                    dir = "/";
+                return await this.file_upload(blob, dir, name);
+            }
+        }
+        catch (error) {
+            const msg = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push("error", `Recursive upload failed for ${localPath}: ${msg}`);
+            return false;
+        }
+    }
+    /**
+     * Performs a dummy upload for testing purposes.
+     * @returns A Promise resolving to true on success, or null if client is missing.
+     */
+    async dummy_upload() {
+        const client = await this.client_get();
+        if (!client) {
+            return null;
+        }
+        // dummy_upload is deprecated/test logic, fixing for compilation
+        const data = {
+            upload_path: this.chrisFolder,
+        };
+        const fileContent = "This is a test file";
+        const fileData = JSON.stringify(fileContent);
+        const uploadFileBlob = new Blob([fileData], {
+            type: "application/json",
+        });
+        const filename = "dummy.json";
+        return await this.file_upload(uploadFileBlob, this.chrisFolder, filename);
+    }
+}
+exports.ChrisIO = ChrisIO;
+/**
+ * Global ChRIS IO instance.
+ */
+exports.chrisIO = new ChrisIO();
+//# sourceMappingURL=chrisIO.js.map

package/dist/io/chrisIO.js.map

@@ -0,0 +1 @@
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package/dist/io/io.d.ts

@@ -0,0 +1,21 @@
+/**
+ * @file Storage-provider abstraction (IStorageProvider) and provider exports.
+ *
+ * Interface for storage providers.
+ * Defines the methods required for a storage provider to be compatible with cumin.
+ */
+export interface IStorageProvider {
+    read(path: string): Promise<string | null>;
+    readBinary(path: string): Promise<ArrayBuffer | null>;
+    write(path: string, data: string): Promise<void>;
+    remove(path: string): Promise<void>;
+    mkdir(path: string, options?: {
+        recursive?: boolean;
+    }): Promise<void>;
+    exists(path: string): Promise<boolean>;
+    readdir(path: string): Promise<string[]>;
+    isDirectory(path: string): Promise<boolean>;
+    join(...paths: string[]): string;
+    basename(path: string): string;
+}
+export { BrowserStorageProvider } from "./browser_io";

package/dist/io/io.js

@@ -0,0 +1,6 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.BrowserStorageProvider = void 0;
+var browser_io_1 = require("./browser_io");
+Object.defineProperty(exports, "BrowserStorageProvider", { enumerable: true, get: function () { return browser_io_1.BrowserStorageProvider; } });
+//# sourceMappingURL=io.js.map

package/dist/io/io.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"io.js","sourceRoot":"","sources":["../../src/io/io.ts"],"names":[],"mappings":";;;AAmBA,2CAAsD;AAA7C,oHAAA,sBAAsB,OAAA"}

package/dist/io/node_io.d.ts

@@ -0,0 +1,30 @@
+/**
+ * @file Node.js implementation of the Storage Provider interface.
+ *
+ * This module provides a concrete implementation of `IStorageProvider` using
+ * Node.js's native `fs` module. It handles file system operations such as
+ * reading, writing, listing directories, and checking file existence.
+ *
+ * @module
+ */
+import { IStorageProvider } from "./io.js";
+/**
+ * NodeStorageProvider implements IStorageProvider using Node.js's native 'fs' module.
+ * It handles file system operations for reading, writing, and removing files,
+ * and creating directories.
+ */
+export declare class NodeStorageProvider implements IStorageProvider {
+    private resolvePath;
+    read(filepath: string): Promise<string | null>;
+    readBinary(filepath: string): Promise<ArrayBuffer | null>;
+    write(filepath: string, data: string): Promise<void>;
+    remove(filepath: string): Promise<void>;
+    mkdir(filepath: string, options?: {
+        recursive?: boolean;
+    }): Promise<void>;
+    exists(filepath: string): Promise<boolean>;
+    readdir(filepath: string): Promise<string[]>;
+    isDirectory(filepath: string): Promise<boolean>;
+    join(...paths: string[]): string;
+    basename(filepath: string): string;
+}