@fnndsc/brasa 0.1.0

package/dist/builtins/fs/pull.js

@@ -0,0 +1,445 @@
+/**
+ * @file Builtin pull command.
+ *
+ * Blocking PACS series retrieve with parallel execution and per-series structured 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 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';
+import { sink_get } from '../../core/sink.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;
+function progressStatus_fromSeries(status, lonkConfirmed) {
+    if (status === 'pulled')
+        return lonkConfirmed ? 'done' : 'unconfirmed';
+    if (status === 'pending' || status === 'pulling')
+        return 'running';
+    return status;
+}
+function pullProgress_emit(task, status, phase = 'watching') {
+    const current = task.actualFiles;
+    const total = task.expectedFiles > 0 ? Math.max(task.expectedFiles, current, 1) : Math.max(current, 1);
+    sink_get().progress_write({
+        operation: 'pull',
+        kind: 'retrieve',
+        phase,
+        itemId: task.seriesUID,
+        label: task.label,
+        current,
+        total,
+        percent: total > 0 ? Math.min(100, (current / total) * 100) : undefined,
+        unit: 'files',
+        status: status ?? progressStatus_fromSeries(task.status, task.lonkConfirmed),
+    });
+}
+function pullProgress_complete(allTasks, failed) {
+    const done = allTasks.filter((t) => t.status === 'pulled').length;
+    sink_get().progress_write({
+        operation: 'pull',
+        kind: 'retrieve',
+        phase: failed ? 'failed' : 'complete',
+        label: failed ? 'Pull incomplete' : 'Pull complete',
+        current: done,
+        total: allTasks.length,
+        percent: allTasks.length > 0 ? (done / allTasks.length) * 100 : 100,
+        unit: 'series',
+        status: failed ? 'error' : 'done',
+    });
+}
+/**
+ * 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) {
+        for (const t of tasks) {
+            if (t.status === 'error')
+                pullProgress_emit(t, 'error');
+        }
+        ws.close();
+        return firingErrors;
+    }
+    for (const t of tasks) {
+        pullProgress_emit(t, t.status === 'error' ? 'error' : 'running');
+    }
+    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;
+                if (t.startTime > 0 && now - t.startTime > SERIES_TIMEOUT_MS) {
+                    t.status = 'timeout';
+                    pullProgress_emit(t, 'timeout');
+                    continue;
+                }
+                if (t.actualFiles > 0 && now - t.lastProgressTime > STALL_TIMEOUT_MS) {
+                    t.status = 'stalled';
+                    pullProgress_emit(t, 'stalled');
+                    continue;
+                }
+                if (t.startTime > 0 && t.actualFiles === 0 && now - t.startTime > NO_ACTIVITY_TIMEOUT_MS) {
+                    t.status = 'pulled';
+                    t.lonkConfirmed = false;
+                    pullProgress_emit(t, 'unconfirmed');
+                    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;
+                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';
+                    pullProgress_emit(t, 'running');
+                }
+                else if ('done' in message && message.done === true) {
+                    t.status = 'pulled';
+                    t.lonkConfirmed = true;
+                    if (t.actualFiles < t.expectedFiles)
+                        t.actualFiles = t.expectedFiles;
+                    pullProgress_emit(t, 'done');
+                }
+                else if ('error' in message && typeof message.error === 'string') {
+                    t.status = 'error';
+                    pullProgress_emit(t, 'error');
+                }
+            }
+            catch {
+                // Malformed message — ignore
+            }
+        });
+        ws.on('error', () => {
+            for (const t of fired) {
+                if (t.status === 'pending' || t.status === 'pulling') {
+                    t.status = 'error';
+                    pullProgress_emit(t, 'error');
+                }
+            }
+            done();
+        });
+        ws.on('close', () => { done(); });
+    });
+    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;
+            pullProgress_emit(t, 'running', 'retrying');
+        }
+        extraFiringErrors += await tasks_pullWatch(retryCandidates, pacsserver, client);
+        retryCandidates = retryCandidates.filter((t) => t.status === 'pulled' && !t.lonkConfirmed);
+    }
+    for (const t of retryCandidates) {
+        t.status = 'error';
+        pullProgress_emit(t, '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;
+    }
+    pullProgress_complete(allTasks, failures.length > 0 || totalFiringErrors > 0);
+}
+/**
+ * Pulls one or more `/net/pacs/queries/...` VFS paths into ChRIS storage.
+ *
+ * Blocking by default: emits per-series structured 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

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

@@ -0,0 +1,10 @@
+import { CommandEnvelope } from '@fnndsc/cumin';
+/**
+ * Reports the current working directory in the ChRIS filesystem context.
+ *
+ * @param args - Command arguments (--title flag supported).
+ * @returns An envelope whose rendered text is the directory (with feed and
+ *   plugin segments replaced by titles under --title) and whose model
+ *   carries the raw path.
+ */
+export declare function builtin_pwd(args?: string[]): Promise<CommandEnvelope>;

package/dist/builtins/fs/pwd.js

@@ -0,0 +1,73 @@
+/**
+ * @file Builtin pwd command.
+ * Reports the current working directory as a command envelope.
+ */
+import { session } from '../../session/index.js';
+import { envelope_ok } from '@fnndsc/cumin';
+import { feeds_list, pluginInstances_list } from '@fnndsc/salsa';
+/**
+ * Reports the current working directory in the ChRIS filesystem context.
+ *
+ * @param args - Command arguments (--title flag supported).
+ * @returns An envelope whose rendered text is the directory (with feed and
+ *   plugin segments replaced by titles under --title) and whose model
+ *   carries the raw path.
+ */
+export async function builtin_pwd(args = []) {
+    const showTitles = args.includes('--title');
+    const cwd = await session.getCWD();
+    const shown = showTitles ? await path_withTitles(cwd) : cwd;
+    return envelope_ok(`${shown}\n`, { kind: 'fs.cwd', data: { path: cwd, shown } });
+}
+/**
+ * Replaces feed_XXXX and pl-<name>_XXXX patterns in a path with their titles.
+ *
+ * @param path - The path to process.
+ * @returns The path with titles replacing directory names.
+ */
+async function path_withTitles(path) {
+    const parts = path.split('/');
+    const replacedParts = await Promise.all(parts.map(async (part) => {
+        // Pattern 1: feed_XXXX
+        const feedMatch = part.match(/^feed_(\d+)$/);
+        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

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

@@ -0,0 +1,37 @@
+import { CommandEnvelope } from '@fnndsc/cumin';
+/**
+ * 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.
+ *
+ * In interactive mode (-i) output is streamed live through the sink so each
+ * confirmation prompt appears in sequence with its result; the envelope then
+ * carries only the model. Otherwise output is buffered into the envelope.
+ *
+ * @param args - Command line arguments (flags and paths).
+ * @returns An envelope whose model lists per-target outcomes.
+ */
+export declare function builtin_rm(args: string[]): Promise<CommandEnvelope>;