@fnndsc/chell 4.3.2 → 5.0.0

package/dist/builtins/fs/pull.args.js

@@ -1,30 +0,0 @@
-/**
- * @file Pure argument parsing for the `pull` builtin.
- *
- * Dependency-free so it is trivially unit-testable.
- *
- * @module
- */
-/**
- * Parses `pull` arguments: the `--nowait` flag, `--retry N`, and path operands.
- *
- * @param args - Raw command arguments.
- * @returns The parsed flags and paths.
- */
-export function pullArgs_parse(args) {
-    const nowait = args.includes('--nowait');
-    let retryMax = 0;
-    const paths = [];
-    for (let i = 0; i < args.length; i++) {
-        if (args[i] === '--retry' && i + 1 < args.length) {
-            const n = parseInt(args[++i], 10);
-            if (!isNaN(n) && n >= 0)
-                retryMax = n;
-        }
-        else if (!args[i].startsWith('--')) {
-            paths.push(args[i]);
-        }
-    }
-    return { nowait, retryMax, paths };
-}
-//# sourceMappingURL=pull.args.js.map

package/dist/builtins/fs/pull.args.js.map

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

@@ -1,26 +0,0 @@
-/**
- * @file Builtin pull command.
- *
- * Blocking PACS series retrieve with parallel execution and per-series MultiBar progress.
- * Accepts one or more `/net/pacs/queries/...` VFS paths (query, study, or series level)
- * and materialises the matching DICOM series into ChRIS storage.
- *
- * Progress is driven by LONK WebSocket push notifications (api/v1/pacs/ws/).
- * Use `--retry N` to automatically re-fire retrieves for series that received no LONK activity.
- *
- * @module
- */
-/**
- * Pulls one or more `/net/pacs/queries/...` VFS paths into ChRIS storage.
- *
- * Blocking by default: shows per-series MultiBar progress via LONK WebSocket,
- * exits non-zero on partial failure.
- * With `--nowait`: fires retrieves and prints `<seriesUID> <retrieveId>` per line, then returns.
- * With `--retry N`: re-fires retrieves for [NO LONK] series up to N additional times.
- *
- * @param args - Command arguments (VFS paths, optional flags).
- * @example
- * pull /net/pacs/queries/42_AccessionNumber:12345678
- * pull --retry 3 /net/pacs/queries/42_AccessionNumber:12345678/Study_1.2.3_US-Hips
- */
-export declare function builtin_pull(args: string[]): Promise<void>;

package/dist/builtins/fs/pull.js

@@ -1,417 +0,0 @@
-/**
- * @file Builtin pull command.
- *
- * Blocking PACS series retrieve with parallel execution and per-series MultiBar progress.
- * Accepts one or more `/net/pacs/queries/...` VFS paths (query, study, or series level)
- * and materialises the matching DICOM series into ChRIS storage.
- *
- * Progress is driven by LONK WebSocket push notifications (api/v1/pacs/ws/).
- * Use `--retry N` to automatically re-fire retrieves for series that received no LONK activity.
- *
- * @module
- */
-import chalk from 'chalk';
-import cliProgress from 'cli-progress';
-import WebSocket from 'ws';
-import { pacsQueries_create, pacsRetrieve_create, } from '@fnndsc/cumin';
-import { session } from '../../session/index.js';
-import { args_checkHasHelpFlag, help_show } from '../help.js';
-import { pacsQuery_createAndWait, queryExpr_parse } from '../net/query.js';
-import { spinner } from '../../lib/spinner.js';
-import { path_resolve } from '../utils.js';
-import { pacs_seriesCollect, pacsServer_resolve, series_cubePathGet, } from '../net/pacsUtils.js';
-import { builtin_cubepath } from '../net/cubepath.js';
-import { pullArgs_parse } from './pull.args.js';
-const STALL_TIMEOUT_MS = 30_000;
-const NO_ACTIVITY_TIMEOUT_MS = 15_000;
-const SERIES_TIMEOUT_MS = 5 * 60 * 1_000;
-const CHECKER_INTERVAL_MS = 2_000;
-/**
- * Walks a VFS path and returns SeriesPullTask array, delegating collection to pacsUtils.
- *
- * @param pathStr - Absolute VFS path to a query, study, or series directory.
- * @param fallbackPacsName - PACS identifier used when RetrieveAETitle is absent.
- * @returns Array of SeriesPullTask ready for firing.
- */
-async function path_seriesCollect(pathStr, fallbackPacsName) {
-    const infos = await pacs_seriesCollect(pathStr, fallbackPacsName, 'pull');
-    return infos.map((info) => ({
-        label: info.label,
-        seriesUID: info.seriesUID,
-        studyUID: info.studyUID,
-        pacsName: info.pacsName,
-        expectedFiles: info.expectedFiles,
-        syntheticQueryId: null,
-        retrieveId: null,
-        status: 'pending',
-        actualFiles: 0,
-        lastProgressFiles: 0,
-        lastProgressTime: Date.now(),
-        startTime: 0,
-        lonkConfirmed: false,
-        cubePathDir: null,
-    }));
-}
-/**
- * Creates a synthetic PACSQuery + PACSRetrieve for a single series.
- *
- * @param task - The pull task to fire (mutated in place: syntheticQueryId, retrieveId, startTime).
- * @param pacsserver - Resolved PACS server ID string.
- */
-async function task_fire(task, pacsserver) {
-    const queryData = {
-        // CUBE rejects duplicate query titles per user, which used to make a
-        // re-pull of the same series fail; a timestamp keeps titles unique.
-        title: `pull_${task.seriesUID}_${Date.now().toString(36)}`,
-        query: JSON.stringify({
-            SeriesInstanceUID: task.seriesUID,
-            StudyInstanceUID: task.studyUID,
-        }),
-        execute: false,
-    };
-    const queryResult = await pacsQueries_create(pacsserver, queryData);
-    if (!queryResult.ok) {
-        task.status = 'error';
-        return;
-    }
-    const syntheticQueryId = queryResult.value.id;
-    const retrieveResult = await pacsRetrieve_create(syntheticQueryId);
-    if (!retrieveResult.ok) {
-        task.status = 'error';
-        return;
-    }
-    task.syntheticQueryId = syntheticQueryId;
-    task.retrieveId = retrieveResult.value.id;
-    task.startTime = Date.now();
-}
-/**
- * Constructs a LONK WebSocket URL from a download token response.
- *
- * @param tokenUrl - The download token resource URL.
- * @param token - The actual download token string.
- * @returns WebSocket URL for the LONK endpoint.
- */
-function lonkWsUrl_build(tokenUrl, token) {
-    return tokenUrl
-        .replace(/^http(s?):\/\//, (_m, s) => `ws${s}://`)
-        .replace(/v1\/downloadtokens\/\d+\//, `v1/pacs/ws/?token=${token}`);
-}
-/**
- * Opens a LONK WebSocket, fires retrieves for the given tasks, and blocks until all
- * tasks reach a terminal state. Mutates each task's status, actualFiles, and lonkConfirmed.
- *
- * @param tasks - Tasks to subscribe, fire, and watch.
- * @param pacsserver - Resolved PACS server identifier.
- * @param client - Authenticated ChRIS API client.
- * @returns Number of tasks that failed to fire their retrieve.
- */
-async function tasks_pullWatch(tasks, pacsserver, client) {
-    const tokenClient = client;
-    const downloadToken = await tokenClient.createDownloadToken();
-    const tokenStr = String(downloadToken.data.token ?? '');
-    const wsUrl = lonkWsUrl_build(downloadToken.url, tokenStr);
-    const ws = new WebSocket(wsUrl);
-    await new Promise((openResolve, openReject) => {
-        ws.once('open', openResolve);
-        ws.once('error', (err) => openReject(err));
-    });
-    for (const t of tasks) {
-        ws.send(JSON.stringify({
-            SeriesInstanceUID: t.seriesUID,
-            pacs_name: t.pacsName,
-            action: 'subscribe',
-        }));
-    }
-    await Promise.all(tasks.map((t) => task_fire(t, pacsserver)));
-    const fired = tasks.filter((t) => t.status !== 'error');
-    const firingErrors = tasks.length - fired.length;
-    if (fired.length === 0) {
-        ws.close();
-        return firingErrors;
-    }
-    const multiBar = new cliProgress.MultiBar({
-        format: ' {label}> [{bar}] {value}/{total}',
-        barCompleteChar: '█',
-        barIncompleteChar: '░',
-        hideCursor: true,
-        clearOnComplete: false,
-        stopOnComplete: false,
-        noTTYOutput: true,
-    }, cliProgress.Presets.shades_classic);
-    const barMap = new Map();
-    for (const t of tasks) {
-        const bar = multiBar.create(Math.max(t.expectedFiles, 1), 0, { label: t.label });
-        barMap.set(t, bar);
-    }
-    const taskByUID = new Map(tasks.map((t) => [t.seriesUID, t]));
-    await new Promise((resolve) => {
-        let resolved = false;
-        const done = () => {
-            if (resolved)
-                return;
-            resolved = true;
-            clearInterval(checker);
-            try {
-                ws.close();
-            }
-            catch { /* ignore */ }
-            resolve();
-        };
-        const checker = setInterval(() => {
-            const now = Date.now();
-            let allTerminal = true;
-            for (const t of fired) {
-                if (t.status === 'pulled' || t.status === 'error' || t.status === 'stalled' || t.status === 'timeout') {
-                    continue;
-                }
-                allTerminal = false;
-                const bar = barMap.get(t);
-                if (t.startTime > 0 && now - t.startTime > SERIES_TIMEOUT_MS) {
-                    t.status = 'timeout';
-                    bar?.update(t.actualFiles, { label: `${t.label} [TIMEOUT]` });
-                    continue;
-                }
-                if (t.actualFiles > 0 && now - t.lastProgressTime > STALL_TIMEOUT_MS) {
-                    t.status = 'stalled';
-                    bar?.update(t.actualFiles, { label: `${t.label} [STALLED]` });
-                    continue;
-                }
-                if (t.startTime > 0 && t.actualFiles === 0 && now - t.startTime > NO_ACTIVITY_TIMEOUT_MS) {
-                    t.status = 'pulled';
-                    t.lonkConfirmed = false;
-                    bar?.update(Math.max(t.expectedFiles, 1), { label: `${t.label} [NO LONK]` });
-                    continue;
-                }
-            }
-            if (allTerminal)
-                done();
-        }, CHECKER_INTERVAL_MS);
-        ws.on('message', (data) => {
-            try {
-                const outer = JSON.parse(data.toString());
-                const seriesUID = outer.SeriesInstanceUID;
-                const message = outer.message;
-                if (!seriesUID || !message)
-                    return;
-                const t = taskByUID.get(seriesUID);
-                if (!t)
-                    return;
-                const bar = barMap.get(t);
-                if ('ndicom' in message && typeof message.ndicom === 'number') {
-                    const n = message.ndicom;
-                    t.actualFiles = n;
-                    t.lastProgressFiles = n;
-                    t.lastProgressTime = Date.now();
-                    if (t.status === 'pending')
-                        t.status = 'pulling';
-                    const total = t.expectedFiles > 0 ? t.expectedFiles : Math.max(n, 1);
-                    bar?.setTotal(total);
-                    bar?.update(n);
-                }
-                else if ('done' in message && message.done === true) {
-                    t.status = 'pulled';
-                    t.lonkConfirmed = true;
-                    const finalTotal = t.expectedFiles > 0 ? t.expectedFiles : t.actualFiles || 1;
-                    bar?.setTotal(finalTotal);
-                    bar?.update(finalTotal, { label: `${t.label} [DONE]` });
-                }
-                else if ('error' in message && typeof message.error === 'string') {
-                    t.status = 'error';
-                    bar?.update(t.actualFiles, { label: `${t.label} [ERROR]` });
-                }
-            }
-            catch {
-                // Malformed message — ignore
-            }
-        });
-        ws.on('error', () => {
-            for (const t of fired) {
-                if (t.status === 'pending' || t.status === 'pulling') {
-                    t.status = 'error';
-                    barMap.get(t)?.update(t.actualFiles, { label: `${t.label} [WS ERROR]` });
-                }
-            }
-            done();
-        });
-        ws.on('close', () => { done(); });
-    });
-    multiBar.stop();
-    return firingErrors;
-}
-/**
- * Resolves raw path/query arguments to concrete `/net/pacs` VFS paths,
- * running PACS queries for query expressions.
- *
- * @param paths - Raw path or query-expression operands.
- * @param pacsserver - The resolved PACS server identifier.
- * @returns The resolved VFS paths.
- */
-async function paths_resolveToVfs(paths, pacsserver) {
-    const resolvedPaths = [];
-    for (const rawPath of paths) {
-        const p = rawPath.startsWith('/') ? rawPath : await path_resolve(rawPath);
-        if (p.startsWith('/net/pacs')) {
-            resolvedPaths.push(p);
-        }
-        else if (queryExpr_parse(rawPath)) {
-            // Query with the RAW expression: path resolution prefixes the CWD,
-            // which would corrupt the first DICOM key (e.g. '/AccessionNumber').
-            spinner.start(`Querying PACS for ${rawPath}...`, true);
-            const qResult = await pacsQuery_createAndWait(rawPath, `pull_${rawPath}`, pacsserver, (msg) => spinner.updateMessage(msg));
-            spinner.stop();
-            if (qResult) {
-                console.log(chalk.gray(`  → ${qResult.vfsPath}`));
-                resolvedPaths.push(qResult.vfsPath);
-            }
-            else {
-                console.error(chalk.red(`pull: Query failed for: ${rawPath}`));
-            }
-        }
-        else {
-            console.error(chalk.red(`pull: Not a PACS VFS path or valid query expression: ${rawPath}`));
-        }
-    }
-    return resolvedPaths;
-}
-/**
- * Re-fires retrieves for series that pulled without LONK confirmation, up to
- * `retryMax` additional attempts, then permanently fails any still unconfirmed.
- *
- * @param allTasks - All pull tasks.
- * @param retryMax - Maximum retry attempts.
- * @param pacsserver - The PACS server identifier.
- * @param client - The connected ChRIS client.
- * @returns The number of additional retrieve-firing errors incurred.
- */
-async function pullRetryLoop(allTasks, retryMax, pacsserver, client) {
-    let extraFiringErrors = 0;
-    let retryCandidates = allTasks.filter((t) => t.status === 'pulled' && !t.lonkConfirmed);
-    const pacsClient = client;
-    for (let attempt = 1; attempt <= retryMax && retryCandidates.length > 0; attempt++) {
-        await Promise.all(retryCandidates.map(async (t) => {
-            const result = await series_cubePathGet(t.seriesUID, pacsClient, 1, 0);
-            if (result) {
-                t.lonkConfirmed = true;
-                t.cubePathDir = result.folderPath;
-            }
-        }));
-        retryCandidates = retryCandidates.filter((t) => !t.lonkConfirmed);
-        if (retryCandidates.length === 0)
-            break;
-        console.log(chalk.yellow(`\nRetry ${attempt}/${retryMax} for ${retryCandidates.length} unconfirmed series...`));
-        for (const t of retryCandidates) {
-            t.status = 'pending';
-            t.actualFiles = 0;
-            t.lastProgressFiles = 0;
-            t.lastProgressTime = Date.now();
-            t.startTime = 0;
-            t.lonkConfirmed = false;
-            t.syntheticQueryId = null;
-            t.retrieveId = null;
-        }
-        extraFiringErrors += await tasks_pullWatch(retryCandidates, pacsserver, client);
-        retryCandidates = retryCandidates.filter((t) => t.status === 'pulled' && !t.lonkConfirmed);
-    }
-    for (const t of retryCandidates) {
-        t.status = 'error';
-    }
-    return extraFiringErrors;
-}
-/**
- * Prints the pull summary and sets a non-zero exit code on any failure.
- *
- * @param allTasks - All pull tasks.
- * @param totalFiringErrors - Count of retrieve-firing errors across all attempts.
- */
-function pullSummary_print(allTasks, totalFiringErrors) {
-    const pulled = allTasks.filter((t) => t.status === 'pulled').length;
-    const totalCount = allTasks.length;
-    const failures = allTasks.filter((t) => t.status !== 'pulled');
-    if (failures.length === 0) {
-        console.log(chalk.green(`\n✓ ${pulled}/${totalCount} series pulled successfully.`));
-    }
-    else {
-        console.log(chalk.yellow(`\n⚠ ${pulled}/${totalCount} series complete.`));
-        for (const f of failures) {
-            console.log(chalk.red(`  ✗ ${f.label} [${f.status.toUpperCase()}]`));
-        }
-        process.exitCode = 1;
-    }
-    if (totalFiringErrors > 0) {
-        console.log(chalk.red(`  ${totalFiringErrors} retrieve(s) failed to start.`));
-        process.exitCode = 1;
-    }
-}
-/**
- * Pulls one or more `/net/pacs/queries/...` VFS paths into ChRIS storage.
- *
- * Blocking by default: shows per-series MultiBar progress via LONK WebSocket,
- * exits non-zero on partial failure.
- * With `--nowait`: fires retrieves and prints `<seriesUID> <retrieveId>` per line, then returns.
- * With `--retry N`: re-fires retrieves for [NO LONK] series up to N additional times.
- *
- * @param args - Command arguments (VFS paths, optional flags).
- * @example
- * pull /net/pacs/queries/42_AccessionNumber:12345678
- * pull --retry 3 /net/pacs/queries/42_AccessionNumber:12345678/Study_1.2.3_US-Hips
- */
-export async function builtin_pull(args) {
-    if (args_checkHasHelpFlag(args, 'pull')) {
-        help_show('pull');
-        return;
-    }
-    const { nowait, retryMax, paths } = pullArgs_parse(args);
-    if (paths.length === 0) {
-        console.error(chalk.red('pull: No paths specified. Usage: pull [--nowait] [--retry N] <vfs-path> [...]'));
-        process.exitCode = 1;
-        return;
-    }
-    const pacsIdentifier = await pacsServer_resolve();
-    if (!pacsIdentifier) {
-        console.error(chalk.red('pull: No PACS server available. Set one with: pacs connect <id>'));
-        process.exitCode = 1;
-        return;
-    }
-    const pacsserver = pacsIdentifier;
-    const resolvedPaths = await paths_resolveToVfs(paths, pacsserver);
-    const allTasks = [];
-    for (const p of resolvedPaths) {
-        const tasks = await path_seriesCollect(p, pacsIdentifier);
-        if (tasks.length === 0) {
-            console.error(chalk.yellow(`pull: No series found under: ${p}`));
-        }
-        allTasks.push(...tasks);
-    }
-    if (allTasks.length === 0) {
-        console.error(chalk.red('pull: No series to retrieve.'));
-        process.exitCode = 1;
-        return;
-    }
-    const client = await session.connection.client_get();
-    if (!client) {
-        console.error(chalk.red('pull: Not connected to ChRIS.'));
-        process.exitCode = 1;
-        return;
-    }
-    // --nowait: fire retrieves and exit without watching
-    if (nowait) {
-        for (const t of allTasks) {
-            await task_fire(t, pacsserver);
-            if (t.retrieveId !== null) {
-                console.log(`${t.seriesUID} ${t.retrieveId}`);
-            }
-            else {
-                console.log(`${t.seriesUID} ERROR`);
-                process.exitCode = 1;
-            }
-        }
-        return;
-    }
-    let totalFiringErrors = await tasks_pullWatch(allTasks, pacsserver, client);
-    totalFiringErrors += await pullRetryLoop(allTasks, retryMax, pacsserver, client);
-    pullSummary_print(allTasks, totalFiringErrors);
-    // Report CUBE paths via cubepath; --retry handles pacsseries DB lag post-pull
-    await builtin_cubepath([...resolvedPaths, '--retry']);
-    console.log(chalk.gray('Detached — use `pacsretrieve report <queryId>` to verify.'));
-}
-//# sourceMappingURL=pull.js.map

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

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

@@ -1,7 +0,0 @@
-/**
- * Prints the current working directory in the ChRIS filesystem context.
- *
- * @param args - Command arguments (--title flag supported).
- * @returns A Promise that resolves when the directory is printed.
- */
-export declare function builtin_pwd(args?: string[]): Promise<void>;

package/dist/builtins/fs/pwd.js

@@ -1,75 +0,0 @@
-/**
- * @file Builtin pwd command.
- * Prints the current working directory.
- */
-import { session } from '../../session/index.js';
-import { feeds_list, pluginInstances_list } from '@fnndsc/salsa';
-/**
- * Prints the current working directory in the ChRIS filesystem context.
- *
- * @param args - Command arguments (--title flag supported).
- * @returns A Promise that resolves when the directory is printed.
- */
-export async function builtin_pwd(args = []) {
-    const showTitles = args.includes('--title');
-    const cwd = await session.getCWD();
-    if (!showTitles) {
-        console.log(cwd);
-        return;
-    }
-    // Replace feed and plugin patterns with titles
-    const titlePath = await path_withTitles(cwd);
-    console.log(titlePath);
-}
-/**
- * Replaces feed_XXXX and pl-<name>_XXXX patterns in a path with their titles.
- *
- * @param path - The path to process.
- * @returns The path with titles replacing directory names.
- */
-async function path_withTitles(path) {
-    const parts = path.split('/');
-    const replacedParts = await Promise.all(parts.map(async (part) => {
-        // Pattern 1: feed_XXXX
-        const feedMatch = part.match(/^feed_(\d+)$/);
-        if (feedMatch) {
-            const feedId = parseInt(feedMatch[1], 10);
-            try {
-                const feedData = await feeds_list({ id: feedId, limit: 1 });
-                if (feedData && feedData.tableData && feedData.tableData.length > 0) {
-                    const feed = feedData.tableData[0];
-                    if (feed && typeof feed.name === 'string') {
-                        return feed.name;
-                    }
-                }
-            }
-            catch (e) {
-                // Silently ignore errors
-            }
-            return part;
-        }
-        // Pattern 2: pl-<name>_XXXX
-        const pluginMatch = part.match(/^(pl-.+)_(\d+)$/);
-        if (pluginMatch) {
-            const pluginInstanceId = parseInt(pluginMatch[2], 10);
-            try {
-                const instanceData = await pluginInstances_list({ id: pluginInstanceId, limit: 1 });
-                if (instanceData && instanceData.tableData && instanceData.tableData.length > 0) {
-                    const instance = instanceData.tableData[0];
-                    if (instance) {
-                        const pluginName = typeof instance.plugin_name === 'string' ? instance.plugin_name : '';
-                        const pluginVersion = typeof instance.plugin_version === 'string' ? instance.plugin_version : '';
-                        return pluginVersion ? `${pluginName} v${pluginVersion}` : pluginName;
-                    }
-                }
-            }
-            catch (e) {
-                // Silently ignore errors
-            }
-            return part;
-        }
-        return part; // Return unchanged if no match
-    }));
-    return replacedParts.join('/');
-}
-//# sourceMappingURL=pwd.js.map

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

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

@@ -1,31 +0,0 @@
-/**
- * Parsed `rm` arguments: flags plus the resolved list of path operands.
- */
-export interface RmArgs {
-    recursive: boolean;
-    force: boolean;
-    interactive: boolean;
-    paths: string[];
-}
-/**
- * Parses `rm` arguments, supporting combined short flags (`-rf`, `-rfi`) and the
- * `--` end-of-options separator.
- *
- * @param args - Raw command arguments.
- * @returns The parsed flags and path operands.
- */
-export declare function rmArgs_parse(args: string[]): RmArgs;
-/**
- * Formats the multi-target removal summary line.
- *
- * @param successCount - Number of items removed successfully.
- * @param failCount - Number of items that failed to remove.
- * @returns The summary string, or null if there is nothing to summarise.
- */
-export declare function rmSummary_format(successCount: number, failCount: number): string | null;
-/**
- * Removes one or more files or directories.
- *
- * @param args - Command line arguments (flags and paths).
- */
-export declare function builtin_rm(args: string[]): Promise<void>;