@fnndsc/chell 4.2.8

package/dist/builtins/fs/cat.js

@@ -0,0 +1,249 @@
+/**
+ * @file Builtin cat command.
+ * Displays file contents.
+ */
+import chalk from 'chalk';
+import { path_resolve, error_stripDebugPrefix } from '../utils.js';
+import { files_cat as chefs_cat_cmd, files_catBinary as chefs_catBinary_cmd } from '@fnndsc/chili/commands/fs/cat.js';
+import { cat_render } from '@fnndsc/chili/views/fs.js';
+import { errorStack } from '@fnndsc/cumin';
+import * as path from 'path';
+/** File extensions that receive syntax highlighting. */
+const HIGHLIGHT_EXTENSIONS = new Set(['.json', '.yaml', '.yml']);
+/**
+ * Applies chalk-based syntax highlighting to JSON content.
+ * Returns the original string if the content is not valid JSON.
+ *
+ * @param content - Raw JSON string.
+ * @returns Highlighted string, or original on parse failure.
+ */
+function json_highlight(content) {
+    try {
+        JSON.parse(content);
+    }
+    catch {
+        return content;
+    }
+    return content.replace(/("(?:\\u[0-9a-fA-F]{4}|\\[^u]|[^\\"])*"(\s*:)?|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+-]?\d+)?)/g, (match) => {
+        if (match.endsWith(':'))
+            return chalk.cyan(match); // key
+        if (match.startsWith('"'))
+            return chalk.green(match); // string value
+        if (match === 'true' || match === 'false')
+            return chalk.yellow(match);
+        if (match === 'null')
+            return chalk.gray(match);
+        return chalk.magenta(match); // number
+    });
+}
+/**
+ * Applies chalk-based syntax highlighting to YAML content line by line.
+ *
+ * @param content - Raw YAML string.
+ * @returns Highlighted string.
+ */
+function yaml_highlight(content) {
+    return content.split('\n').map((line) => {
+        if (/^\s*#/.test(line))
+            return chalk.gray(line);
+        const kv = line.match(/^(\s*)([\w./-]+)(\s*:\s*)(.*)/);
+        if (kv) {
+            const [, indent, key, sep, value] = kv;
+            const coloredValue = value_yamlColor(value);
+            return `${indent}${chalk.cyan(key)}${chalk.gray(sep)}${coloredValue}`;
+        }
+        const listItem = line.match(/^(\s*-\s+)(.*)/);
+        if (listItem) {
+            return `${chalk.gray(listItem[1])}${chalk.green(listItem[2])}`;
+        }
+        return line;
+    }).join('\n');
+}
+/**
+ * Colors a scalar YAML value based on its type.
+ *
+ * @param value - The raw value string from a YAML key: value line.
+ * @returns Chalk-colored value string.
+ */
+function value_yamlColor(value) {
+    if (!value)
+        return value;
+    if (value === 'true' || value === 'false')
+        return chalk.yellow(value);
+    if (value === 'null' || value === '~')
+        return chalk.gray(value);
+    if (/^-?\d+(\.\d+)?$/.test(value))
+        return chalk.magenta(value);
+    if (/^["']/.test(value))
+        return chalk.green(value);
+    return chalk.white(value);
+}
+/**
+ * Applies syntax highlighting to text content based on file extension.
+ * Returns the original string unchanged when stdout is not a TTY (piping).
+ *
+ * @param content - File content string.
+ * @param filePath - Full path used to determine the file type.
+ * @returns Highlighted or original content.
+ */
+function content_highlight(content, filePath) {
+    if (!process.stdout.isTTY)
+        return content;
+    const ext = path.extname(filePath).toLowerCase();
+    if (ext === '.json')
+        return json_highlight(content);
+    if (ext === '.yaml' || ext === '.yml')
+        return yaml_highlight(content);
+    return content;
+}
+/**
+ * List of file extensions that are considered binary.
+ */
+const BINARY_EXTENSIONS = new Set([
+    '.dcm', // DICOM medical images
+    '.png', '.jpg', '.jpeg', '.gif', '.bmp', '.ico', '.webp', // Images
+    '.pdf', // Documents
+    '.zip', '.tar', '.gz', '.bz2', '.xz', '.7z', '.rar', // Archives
+    '.exe', '.dll', '.so', '.dylib', '.bin', // Executables/Libraries
+    '.mp3', '.mp4', '.avi', '.mov', '.wav', '.flac', // Media
+]);
+/**
+ * Checks if a file path has a binary extension.
+ *
+ * @param filePath - The file path to check.
+ * @returns True if the file has a binary extension.
+ */
+function extension_isBinary(filePath) {
+    const ext = path.extname(filePath).toLowerCase();
+    return BINARY_EXTENSIONS.has(ext);
+}
+/**
+ * Writes a buffer to stdout with proper backpressure handling.
+ *
+ * Splits large buffers into 64KB chunks and waits for drain events when the
+ * output buffer is full. This prevents data loss when piping large binary files
+ * to external commands. Waits for all data to be flushed before resolving.
+ *
+ * @param buffer - The buffer to write to stdout.
+ * @returns A Promise that resolves when all data has been written and flushed.
+ *
+ * @example
+ * ```typescript
+ * const dicomData: Buffer = await fetchDicomFile();
+ * await buffer_writeToStdout(dicomData);
+ * ```
+ */
+async function buffer_writeToStdout(buffer) {
+    return new Promise((resolve, reject) => {
+        if (buffer.length === 0) {
+            resolve();
+            return;
+        }
+        let offset = 0;
+        const chunkSize = 64 * 1024; // 64KB chunks
+        /**
+         * Recursively writes the next chunk of data to stdout.
+         * Handles backpressure by waiting for drain events when buffer is full.
+         */
+        const chunk_writeNext = () => {
+            try {
+                while (offset < buffer.length) {
+                    const end = Math.min(offset + chunkSize, buffer.length);
+                    const chunk = buffer.subarray(offset, end);
+                    offset = end;
+                    const canContinue = process.stdout.write(chunk);
+                    if (!canContinue) {
+                        // Buffer is full, wait for drain event
+                        process.stdout.once('drain', chunk_writeNext);
+                        return;
+                    }
+                }
+                // All chunks written - ensure stdout is flushed before resolving
+                // Writing an empty string forces a flush check. If write() returns false,
+                // the buffer is full and we must wait for drain. This prevents truncation
+                // when piping to external processes, as Node.js won't exit until we resolve.
+                if (process.stdout.write('')) {
+                    // Buffer has space, all data is flushed
+                    resolve();
+                }
+                else {
+                    // Buffer is full, wait for final drain before resolving
+                    process.stdout.once('drain', () => resolve());
+                }
+            }
+            catch (err) {
+                reject(err);
+            }
+        };
+        chunk_writeNext();
+    });
+}
+/**
+ * Displays the content of one or more files.
+ *
+ * Supports multiple files and concatenates their output. Binary mode is applied
+ * consistently to all files if any file is detected as binary or --binary is specified.
+ *
+ * @param args - Command line arguments (file paths and optional --binary flag).
+ *
+ * @example
+ * ```typescript
+ * await builtin_cat(['file1.txt', 'file2.txt']);
+ * await builtin_cat(['--binary', 'image.dcm']);
+ * await builtin_cat(['*.json']);  // After wildcard expansion
+ * ```
+ */
+export async function builtin_cat(args) {
+    let binaryMode = false;
+    const filePaths = [];
+    for (const arg of args) {
+        if (arg === '--binary') {
+            binaryMode = true;
+        }
+        else {
+            filePaths.push(arg);
+        }
+    }
+    if (filePaths.length === 0) {
+        console.error(chalk.red('Usage: cat [--binary] <file> [file...]'));
+        return;
+    }
+    for (let i = 0; i < filePaths.length; i++) {
+        const pathArg = filePaths[i];
+        const target = await path_resolve(pathArg);
+        // Auto-detect binary files
+        const isBinaryFile = extension_isBinary(target);
+        // Inform user about auto-detection only if in interactive mode (stdout is TTY)
+        // Don't show warning when piping, as it would corrupt the binary output
+        // Only show on first file to avoid spam
+        if (i === 0 && isBinaryFile && !binaryMode && process.stdout.isTTY) {
+            console.error(chalk.cyan(`Info: ${pathArg} detected as binary file (${path.extname(target)}), using binary mode.`));
+            console.error(chalk.cyan('Tip: Use "cat --binary <file>" to explicitly request binary mode.'));
+            console.error('');
+        }
+        // Use binary mode if requested OR if file is detected as binary
+        if (binaryMode || isBinaryFile) {
+            const result = await chefs_catBinary_cmd(target);
+            if (!result.ok) {
+                const error = errorStack.stack_pop();
+                console.error(chalk.red(`cat: ${pathArg}: ${error ? error_stripDebugPrefix(error.message) : 'Unknown error'}`));
+                process.exitCode = 1;
+                continue;
+            }
+            // Output raw buffer to stdout with backpressure handling
+            await buffer_writeToStdout(result.value);
+        }
+        else {
+            const result = await chefs_cat_cmd(target);
+            if (!result.ok) {
+                const error = errorStack.stack_pop();
+                console.error(chalk.red(`cat: ${pathArg}: ${error ? error_stripDebugPrefix(error.message) : 'Unknown error'}`));
+                process.exitCode = 1;
+                continue;
+            }
+            const highlighted = content_highlight(result.value, target);
+            console.log(cat_render(highlighted, pathArg));
+        }
+    }
+}
+//# sourceMappingURL=cat.js.map

package/dist/builtins/fs/cat.js.map

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package/dist/builtins/fs/cd.d.ts

@@ -0,0 +1,41 @@
+/**
+ * Interface representing a FileBrowserFolder from ChRIS API.
+ */
+interface FileBrowserFolder {
+    path?: string;
+    data?: {
+        path?: string;
+    };
+}
+/**
+ * Normalizes a logical path for VFS comparison by stripping a single trailing
+ * slash (except for the root path).
+ *
+ * @param logicalPath - The resolved logical path.
+ * @returns The normalized path.
+ */
+export declare function vfsPath_normalize(logicalPath: string): string;
+/**
+ * Reports whether a path is a structural VFS container (always valid).
+ *
+ * @param cleanPath - The normalized path.
+ * @returns True if the path is a known structural VFS container.
+ */
+export declare function vfsPath_isStructural(cleanPath: string): boolean;
+/**
+ * Verifies if a given FileBrowserFolder object exactly matches the validation path.
+ *
+ * @param folder - The FileBrowserFolder object to verify.
+ * @param validationPath - The path to match against.
+ * @returns True if the folder path exactly matches validationPath, false otherwise.
+ */
+export declare function folder_verifyPathMatch(folder: FileBrowserFolder | null | undefined, validationPath: string): boolean;
+/**
+ * Changes the current working directory in the ChRIS filesystem context.
+ * Validates the existence of the target path before setting it.
+ *
+ * @param args - An array containing the target path as the first element.
+ * @returns A Promise that resolves when the operation is complete.
+ */
+export declare function builtin_cd(args: string[]): Promise<void>;
+export {};

package/dist/builtins/fs/cd.js

@@ -0,0 +1,178 @@
+/**
+ * @file Builtin cd command.
+ * Changes the current working directory.
+ */
+import chalk from 'chalk';
+import { session } from '../../session/index.js';
+import { path_resolve, path_resolveLinks, error_stripDebugPrefix } from '../utils.js';
+/**
+ * Structural VFS container paths that exist by definition and need no API
+ * validation when `cd`-ing into them.
+ */
+const STRUCTURAL_VFS_PATHS = ['/', '/net', '/net/pacs', '/net/pacs/queries', '/proc', '/proc/jobs'];
+/**
+ * Normalizes a logical path for VFS comparison by stripping a single trailing
+ * slash (except for the root path).
+ *
+ * @param logicalPath - The resolved logical path.
+ * @returns The normalized path.
+ */
+export function vfsPath_normalize(logicalPath) {
+    return logicalPath.endsWith('/') && logicalPath.length > 1 ? logicalPath.slice(0, -1) : logicalPath;
+}
+/**
+ * Reports whether a path is a structural VFS container (always valid).
+ *
+ * @param cleanPath - The normalized path.
+ * @returns True if the path is a known structural VFS container.
+ */
+export function vfsPath_isStructural(cleanPath) {
+    return STRUCTURAL_VFS_PATHS.includes(cleanPath);
+}
+/**
+ * Verifies if a given FileBrowserFolder object exactly matches the validation path.
+ *
+ * @param folder - The FileBrowserFolder object to verify.
+ * @param validationPath - The path to match against.
+ * @returns True if the folder path exactly matches validationPath, false otherwise.
+ */
+export function folder_verifyPathMatch(folder, validationPath) {
+    if (!folder) {
+        return false;
+    }
+    const folderPath = folder.data?.path || folder.path || '';
+    // Normalize both by removing all leading and trailing slashes to be robust against API inconsistencies
+    const cleanFolder = folderPath.replace(/^\/+|\/+$/g, '');
+    const cleanValidation = validationPath.replace(/^\/+|\/+$/g, '');
+    return cleanFolder === cleanValidation;
+}
+/**
+ * Handles `cd` into a virtual (VFS) path: structural containers are accepted
+ * directly, deeper VFS paths are validated and their listing cached.
+ *
+ * @param cleanPath - The normalized virtual path.
+ * @param pathArg - The original user-supplied path (for error messages).
+ */
+async function cdVirtual_handle(cleanPath, pathArg) {
+    if (vfsPath_isStructural(cleanPath)) {
+        await session.setCWD(cleanPath);
+        return;
+    }
+    // For deeper VFS paths (e.g. /net/pacs/queries/<id>), validate and cache the
+    // result so a subsequent `ls` doesn't need to re-fetch.
+    const { vfsDispatcher } = await import('@fnndsc/salsa');
+    const listResult = await vfsDispatcher.list(cleanPath);
+    if (!listResult.ok) {
+        const { errorStack } = await import('@fnndsc/cumin');
+        const lastError = errorStack.stack_pop();
+        const detail = lastError ? error_stripDebugPrefix(lastError.message) : 'No such file or directory';
+        console.error(chalk.red(`cd: ${pathArg}: ${detail}`));
+        return;
+    }
+    const { listCache_get } = await import('@fnndsc/cumin');
+    listCache_get().cache_set(cleanPath, listResult.value);
+    await session.setCWD(cleanPath);
+}
+/**
+ * Handles `cd` into a real (API-backed) ChRIS folder: resolves the validation
+ * path, then confirms the folder exists with an exact path match before setting
+ * the working directory.
+ *
+ * @param logicalPath - The resolved logical path.
+ * @param pathArg - The original user-supplied path (for error messages).
+ */
+async function cdReal_handle(logicalPath, pathArg) {
+    const client = await session.connection.client_get();
+    if (!client) {
+        console.error(chalk.red('Not connected to ChRIS.'));
+        return;
+    }
+    let validationPath;
+    if (session.physicalMode_get()) {
+        validationPath = await path_resolveLinks(logicalPath);
+    }
+    else {
+        const { logical_toPhysical } = await import('@fnndsc/chili/utils');
+        const physicalResult = await logical_toPhysical(logicalPath);
+        if (!physicalResult.ok) {
+            console.error(chalk.red(`cd: ${pathArg}: No such file or directory`));
+            if (session.connection.config?.debug) {
+                console.error(chalk.gray(`  Logical path: ${logicalPath}`));
+            }
+            return;
+        }
+        validationPath = physicalResult.value;
+    }
+    if (session.connection.config?.debug) {
+        console.log(chalk.gray(`cd: ${pathArg} → logical: ${logicalPath} → validation: ${validationPath}`));
+    }
+    const cwdPath = session.physicalMode_get() ? validationPath : logicalPath;
+    const currentCwd = await session.getCWD();
+    if (currentCwd === cwdPath) {
+        if (session.connection.config?.debug) {
+            console.log(chalk.gray(`  Already in target directory, skipping validation`));
+        }
+        return;
+    }
+    try {
+        const folder = (await client.getFileBrowserFolderByPath(validationPath));
+        if (folder_verifyPathMatch(folder, validationPath)) {
+            await session.setCWD(cwdPath);
+        }
+        else {
+            console.error(chalk.red(`cd: ${pathArg}: No such file or directory`));
+            if (session.connection.config?.debug) {
+                if (!folder) {
+                    console.error(chalk.gray(`  API returned null for path: ${validationPath}`));
+                }
+                else {
+                    const folderPath = folder.data?.path || folder.path;
+                    console.error(chalk.gray(`  API returned mismatched folder path: ${folderPath} (expected: ${validationPath})`));
+                }
+            }
+        }
+    }
+    catch (apiError) {
+        console.error(chalk.red(`cd: ${pathArg}: No such file or directory`));
+        if (session.connection.config?.debug) {
+            const msg = apiError instanceof Error ? apiError.message : String(apiError);
+            console.error(chalk.gray(`  API error: ${msg}`));
+        }
+    }
+}
+/**
+ * Changes the current working directory in the ChRIS filesystem context.
+ * Validates the existence of the target path before setting it.
+ *
+ * @param args - An array containing the target path as the first element.
+ * @returns A Promise that resolves when the operation is complete.
+ */
+export async function builtin_cd(args) {
+    const pathArg = args.length > 0 ? args.join(' ') : undefined;
+    // 'cd' with no args goes to home
+    if (!pathArg) {
+        return builtin_cd(['~']);
+    }
+    try {
+        const logicalPath = await path_resolve(pathArg);
+        const { vfsDispatcher } = await import('@fnndsc/salsa');
+        const cleanPath = vfsPath_normalize(logicalPath);
+        // Treat the path as virtual if it is, or is a parent of, any registered
+        // provider prefix (e.g. /proc is parent of /proc/feeds).
+        const isParentOfVfs = vfsDispatcher.providers_get().some((p) => p.prefix.startsWith(cleanPath + '/'));
+        const isVirtual = cleanPath === '/' ||
+            cleanPath === '/net' ||
+            isParentOfVfs ||
+            vfsDispatcher.provider_get(cleanPath).prefix !== '';
+        if (isVirtual) {
+            await cdVirtual_handle(cleanPath, pathArg);
+            return;
+        }
+        await cdReal_handle(logicalPath, pathArg);
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        console.error(chalk.red(`Failed to cd: ${msg}`));
+    }
+}
+//# sourceMappingURL=cd.js.map

package/dist/builtins/fs/cd.js.map

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package/dist/builtins/fs/cp.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Copies a file or directory.
+ * Supports multiple sources when destination is a directory.
+ *
+ * @param args - [flags, src1, src2, ..., dest]
+ */
+export declare function builtin_cp(args: string[]): Promise<void>;

package/dist/builtins/fs/cp.js

@@ -0,0 +1,73 @@
+/**
+ * @file Builtin cp command.
+ * Copies files or directories.
+ */
+import chalk from 'chalk';
+import path from 'path';
+import { commandArgs_process, path_resolve } from '../utils.js';
+import { files_cp as chefs_cp_cmd } from '@fnndsc/chili/commands/fs/cp.js';
+import { cp_render } from '@fnndsc/chili/views/fs.js';
+import { listCache_get } from '@fnndsc/cumin';
+/**
+ * Copies a file or directory.
+ * Supports multiple sources when destination is a directory.
+ *
+ * @param args - [flags, src1, src2, ..., dest]
+ */
+export async function builtin_cp(args) {
+    const parsed = commandArgs_process(args);
+    const pathArgs = parsed._;
+    if (pathArgs.length < 2) {
+        console.log(chalk.red('Usage: cp [-r] <source...> <dest>'));
+        return;
+    }
+    const recursive = !!parsed['r'] || !!parsed['recursive'];
+    // Last arg is destination, all others are sources
+    const dest = pathArgs[pathArgs.length - 1];
+    const sources = pathArgs.slice(0, -1);
+    const destPath = await path_resolve(dest);
+    const listCache = listCache_get();
+    let successCount = 0;
+    let failCount = 0;
+    for (const src of sources) {
+        try {
+            const srcPath = await path_resolve(src);
+            // For multiple sources, show which file we're copying
+            if (sources.length > 1) {
+                console.log(chalk.gray(`Copying ${srcPath}...`));
+            }
+            else {
+                console.log(`Copying ${srcPath} to ${destPath}...`);
+            }
+            const success = await chefs_cp_cmd(srcPath, destPath, { recursive });
+            if (sources.length === 1) {
+                console.log(cp_render(srcPath, destPath, success));
+            }
+            if (success) {
+                successCount++;
+            }
+            else {
+                failCount++;
+            }
+        }
+        catch (e) {
+            const msg = e instanceof Error ? e.message : String(e);
+            console.error(chalk.red(`cp: ${src}: ${msg}`));
+            failCount++;
+        }
+    }
+    // Invalidate destination directory (always, since files copied into it)
+    listCache.cache_invalidate(destPath);
+    const destParent = path.posix.dirname(destPath);
+    listCache.cache_invalidate(destParent);
+    // Summary for multiple files
+    if (sources.length > 1) {
+        if (failCount === 0) {
+            console.log(chalk.green(`✓ Copied ${successCount} file(s) to ${destPath}`));
+        }
+        else {
+            console.log(chalk.yellow(`⚠ Copied ${successCount} file(s), ${failCount} failed`));
+        }
+    }
+}
+//# sourceMappingURL=cp.js.map

package/dist/builtins/fs/cp.js.map

@@ -0,0 +1 @@
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package/dist/builtins/fs/download.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Downloads a remote ChRIS file or directory to the local filesystem.
+ *
+ * @param args - [remotePath, localPath] plus optional -f/--force to overwrite.
+ */
+export declare function builtin_download(args: string[]): Promise<void>;

package/dist/builtins/fs/download.js

@@ -0,0 +1,41 @@
+/**
+ * @file Builtin download command.
+ * Downloads files from ChRIS to the local filesystem with progress.
+ */
+import chalk from 'chalk';
+import path from 'path';
+import { path_resolve } from '../utils.js';
+import { files_downloadWithProgress as chefs_download_cmd, bytes_format } from '@fnndsc/chili/commands/fs/download.js';
+/**
+ * Downloads a remote ChRIS file or directory to the local filesystem.
+ *
+ * @param args - [remotePath, localPath] plus optional -f/--force to overwrite.
+ */
+export async function builtin_download(args) {
+    const force = args.includes('-f') || args.includes('--force');
+    const cleanArgs = args.filter(arg => arg !== '-f' && arg !== '--force');
+    if (cleanArgs.length < 2) {
+        console.log(chalk.red('Usage: download <remote_path> <local_path> [-f|--force]'));
+        return;
+    }
+    const remotePathArg = cleanArgs[0];
+    const localPathArg = cleanArgs[1];
+    const targetRemote = await path_resolve(remotePathArg);
+    const targetLocal = path.resolve(localPathArg);
+    try {
+        const summary = await chefs_download_cmd(targetRemote, targetLocal, { force });
+        console.log('');
+        if (summary.failedCount === 0) {
+            console.log(chalk.green(`✓ Successfully downloaded ${summary.transferredCount} file(s)`));
+        }
+        else {
+            console.log(chalk.yellow(`⚠ Downloaded ${summary.transferredCount} file(s), ${summary.failedCount} failed`));
+        }
+        console.log(chalk.gray(`  Total: ${bytes_format(summary.transferSize)} in ${summary.duration.toFixed(1)}s (${bytes_format(summary.speed)}/s)`));
+    }
+    catch (e) {
+        const msg = e instanceof Error ? e.message : String(e);
+        console.error(chalk.red(`Download error: ${msg}`));
+    }
+}
+//# sourceMappingURL=download.js.map

package/dist/builtins/fs/download.js.map

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