@fnndsc/brasa 0.1.0

package/dist/builtins/help.js.map

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

@@ -0,0 +1,45 @@
+/**
+ * @file Builtin index.
+ * Re-exports all built-in commands.
+ */
+export * from './fs/cd.js';
+export * from './fs/pwd.js';
+export * from './fs/ls.js';
+export * from './fs/cp.js';
+export * from './fs/mv.js';
+export * from './fs/rm.js';
+export * from './fs/cat.js';
+export * from './fs/mkdir.js';
+export * from './fs/touch.js';
+export * from './fs/upload.js';
+export * from './fs/pull.js';
+export * from './fs/download.js';
+export * from './fs/edit.js';
+export * from './fs/tree.js';
+export * from './fs/du.js';
+export * from './net/connect.js';
+export * from './net/logout.js';
+export * from './net/pacs.js';
+export * from './net/query.js';
+export * from './net/cubepath.js';
+export * from './sys/context.js';
+export * from './sys/physicalmode.js';
+export * from './sys/timing.js';
+export * from './sys/version.js';
+export * from './sys/whoami.js';
+export * from './debug.js';
+export * from './help.js';
+export * from './res/plugin.js';
+export * from './res/pipeline.js';
+export * from './res/feed.js';
+export * from './res/files.js';
+export * from './res/compute.js';
+export * from './res/tag.js';
+export * from './res/group.js';
+export * from './res/pluginmeta.js';
+export * from './res/plugininstance.js';
+export * from './res/workflow.js';
+export * from './parametersofplugin.js';
+export * from './store.js';
+export { commandArgs_process, path_resolve, path_resolvePure, error_stripDebugPrefix } from './utils.js';
+export type { ParsedArgs } from './utils.js';

package/dist/builtins/index.js

@@ -0,0 +1,45 @@
+/**
+ * @file Builtin index.
+ * Re-exports all built-in commands.
+ */
+export * from './fs/cd.js';
+export * from './fs/pwd.js';
+export * from './fs/ls.js';
+export * from './fs/cp.js';
+export * from './fs/mv.js';
+export * from './fs/rm.js';
+export * from './fs/cat.js';
+export * from './fs/mkdir.js';
+export * from './fs/touch.js';
+export * from './fs/upload.js';
+export * from './fs/pull.js';
+export * from './fs/download.js';
+export * from './fs/edit.js';
+export * from './fs/tree.js';
+export * from './fs/du.js';
+export * from './net/connect.js';
+export * from './net/logout.js';
+export * from './net/pacs.js';
+export * from './net/query.js';
+export * from './net/cubepath.js';
+export * from './sys/context.js';
+export * from './sys/physicalmode.js';
+export * from './sys/timing.js';
+export * from './sys/version.js';
+export * from './sys/whoami.js';
+export * from './debug.js';
+export * from './help.js';
+export * from './res/plugin.js';
+export * from './res/pipeline.js';
+export * from './res/feed.js';
+export * from './res/files.js';
+export * from './res/compute.js';
+export * from './res/tag.js';
+export * from './res/group.js';
+export * from './res/pluginmeta.js';
+export * from './res/plugininstance.js';
+export * from './res/workflow.js';
+export * from './parametersofplugin.js';
+export * from './store.js';
+export { commandArgs_process, path_resolve, path_resolvePure, error_stripDebugPrefix } from './utils.js';
+//# sourceMappingURL=index.js.map

package/dist/builtins/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/builtins/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,cAAc,YAAY,CAAC;AAC3B,cAAc,aAAa,CAAC;AAC5B,cAAc,YAAY,CAAC;AAC3B,cAAc,YAAY,CAAC;AAC3B,cAAc,YAAY,CAAC;AAC3B,cAAc,YAAY,CAAC;AAC3B,cAAc,aAAa,CAAC;AAC5B,cAAc,eAAe,CAAC;AAC9B,cAAc,eAAe,CAAC;AAC9B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,cAAc,CAAC;AAC7B,cAAc,kBAAkB,CAAC;AACjC,cAAc,cAAc,CAAC;AAC7B,cAAc,cAAc,CAAC;AAC7B,cAAc,YAAY,CAAC;AAE3B,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,eAAe,CAAC;AAC9B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,mBAAmB,CAAC;AAElC,cAAc,kBAAkB,CAAC;AACjC,cAAc,uBAAuB,CAAC;AACtC,cAAc,iBAAiB,CAAC;AAChC,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,YAAY,CAAC;AAC3B,cAAc,WAAW,CAAC;AAE1B,cAAc,iBAAiB,CAAC;AAChC,cAAc,mBAAmB,CAAC;AAClC,cAAc,eAAe,CAAC;AAC9B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,kBAAkB,CAAC;AACjC,cAAc,cAAc,CAAC;AAC7B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,yBAAyB,CAAC;AACxC,cAAc,mBAAmB,CAAC;AAClC,cAAc,yBAAyB,CAAC;AACxC,cAAc,YAAY,CAAC;AAE3B,OAAO,EAAE,mBAAmB,EAAE,YAAY,EAAE,gBAAgB,EAAE,sBAAsB,EAAE,MAAM,YAAY,CAAC"}

package/dist/builtins/net/connect.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Connects to a ChRIS CUBE instance using provided credentials.
+ *
+ * @param args - An array of arguments containing user, password, and URL.
+ * @returns A Promise that resolves when the connection attempt is complete.
+ */
+export declare function builtin_connect(args: string[]): Promise<void>;

package/dist/builtins/net/connect.js

@@ -0,0 +1,42 @@
+/**
+ * @file Builtin connect command.
+ * Establishes a connection to ChRIS.
+ */
+import chalk from 'chalk';
+import { commandArgs_process } from '../utils.js';
+import { connect_login } from '@fnndsc/chili/commands/connect/login.js';
+import { login_render } from '@fnndsc/chili/views/connect.js';
+import { session } from '../../session/index.js';
+import { chrisContext } from '@fnndsc/cumin';
+/**
+ * Connects to a ChRIS CUBE instance using provided credentials.
+ *
+ * @param args - An array of arguments containing user, password, and URL.
+ * @returns A Promise that resolves when the connection attempt is complete.
+ */
+export async function builtin_connect(args) {
+    const parsed = commandArgs_process(args);
+    const user = parsed.user;
+    const password = parsed.password;
+    const url = parsed._[0];
+    if (user && password && url) {
+        try {
+            const success = await connect_login({ user, password, url, debug: false });
+            if (success) {
+                session.offline = false;
+                // Refresh context to update prompt with new user/url
+                await chrisContext.currentContext_update();
+            }
+            console.log(login_render(success, url, user));
+        }
+        catch (error) {
+            const msg = error instanceof Error ? error.message : String(error);
+            console.log(login_render(false, url, user));
+            console.error(chalk.red(`Connection failed: ${msg}`));
+        }
+    }
+    else {
+        console.log(chalk.red('Usage: connect --user <username> --password <password> <url>'));
+    }
+}
+//# sourceMappingURL=connect.js.map

package/dist/builtins/net/connect.js.map

@@ -0,0 +1 @@
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package/dist/builtins/net/cubepath.d.ts

@@ -0,0 +1,18 @@
+/**
+ * @file Builtin cubepath command.
+ *
+ * Given one or more `/net/pacs/queries/...` VFS paths (at query, study, or series level),
+ * resolves where each matching series lives in CUBE storage and reports the
+ * actual file count there. Zero files means the series has not been pulled.
+ *
+ * @module
+ */
+/**
+ * Resolves CUBE FS paths and file counts for all series under one or more PACS VFS paths.
+ *
+ * @param args - `<vfs-path> [...] [--pacsserver <id>] [--retry]`
+ * @example
+ * cubepath /net/pacs/queries/AccessionNumber:12345678_qid:2661
+ * cubepath /net/pacs/queries/.../Series_1.2.3_AX_T2 /net/pacs/queries/.../Series_1.2.3_DWI
+ */
+export declare function builtin_cubepath(args: string[]): Promise<void>;

package/dist/builtins/net/cubepath.js

@@ -0,0 +1,102 @@
+/**
+ * @file Builtin cubepath command.
+ *
+ * Given one or more `/net/pacs/queries/...` VFS paths (at query, study, or series level),
+ * resolves where each matching series lives in CUBE storage and reports the
+ * actual file count there. Zero files means the series has not been pulled.
+ *
+ * @module
+ */
+import chalk from 'chalk';
+import { session } from '../../session/index.js';
+import { args_checkHasHelpFlag, help_show } from '../help.js';
+import { path_resolve } from '../utils.js';
+import { pacs_seriesCollect, pacsServer_resolve, series_cubePathGet, } from './pacsUtils.js';
+/**
+ * Resolves CUBE FS paths and file counts for all series under one or more PACS VFS paths.
+ *
+ * @param args - `<vfs-path> [...] [--pacsserver <id>] [--retry]`
+ * @example
+ * cubepath /net/pacs/queries/AccessionNumber:12345678_qid:2661
+ * cubepath /net/pacs/queries/.../Series_1.2.3_AX_T2 /net/pacs/queries/.../Series_1.2.3_DWI
+ */
+export async function builtin_cubepath(args) {
+    if (args_checkHasHelpFlag(args, 'cubepath')) {
+        help_show('cubepath');
+        return;
+    }
+    let pacsserverOverride = null;
+    let retry = false;
+    const positional = [];
+    for (let i = 0; i < args.length; i++) {
+        if (args[i] === '--pacsserver' && i + 1 < args.length) {
+            pacsserverOverride = args[++i];
+        }
+        else if (args[i] === '--retry') {
+            retry = true;
+        }
+        else if (!args[i].startsWith('--')) {
+            positional.push(args[i]);
+        }
+    }
+    if (positional.length === 0) {
+        console.error(chalk.red('cubepath: Missing path. Usage: cubepath <vfs-path> [...]'));
+        process.exitCode = 1;
+        return;
+    }
+    const pacsIdentifier = await pacsServer_resolve(pacsserverOverride);
+    if (!pacsIdentifier) {
+        console.error(chalk.red('cubepath: No PACS server available. Set one with: pacs connect <id>'));
+        process.exitCode = 1;
+        return;
+    }
+    // Collect series from all paths
+    const allSeries = [];
+    for (const rawPath of positional) {
+        const vfsPath = rawPath.startsWith('/') ? rawPath : await path_resolve(rawPath);
+        if (!vfsPath.startsWith('/net/pacs')) {
+            console.error(chalk.red(`cubepath: Not a PACS VFS path: ${rawPath}`));
+            continue;
+        }
+        const found = await pacs_seriesCollect(vfsPath, pacsIdentifier, 'cubepath');
+        allSeries.push(...found);
+    }
+    if (allSeries.length === 0) {
+        console.error(chalk.yellow('cubepath: No series found under that path.'));
+        process.exitCode = 1;
+        return;
+    }
+    const client = await session.connection.client_get();
+    if (!client) {
+        console.error(chalk.red('cubepath: Not connected to ChRIS.'));
+        process.exitCode = 1;
+        return;
+    }
+    const pacsClient = client;
+    const maxAttempts = retry ? 4 : 1;
+    const retryDelayMs = retry ? 2_000 : 0;
+    const results = await Promise.all(allSeries.map(async (info) => {
+        const cubePath = await series_cubePathGet(info.seriesUID, pacsClient, maxAttempts, retryDelayMs);
+        return { info, cubePath };
+    }));
+    const maxLabelLen = Math.max(...results.map((r) => r.info.seriesLabel.length));
+    let notInCube = 0;
+    for (const { info, cubePath } of results) {
+        const label = info.seriesLabel.padEnd(maxLabelLen);
+        const arrow = chalk.cyan('->');
+        if (cubePath) {
+            const countStr = cubePath.fileCount > 0
+                ? chalk.green(`(${cubePath.fileCount} files)`)
+                : chalk.yellow('(0 files — may not be pulled)');
+            console.log(`  ${chalk.white(label)}  ${arrow}  ${chalk.cyan(cubePath.folderPath)}  ${countStr}`);
+        }
+        else {
+            console.log(`  ${chalk.white(label)}  ${arrow}  ${chalk.gray('(not in CUBE)')}`);
+            notInCube++;
+        }
+    }
+    if (notInCube > 0) {
+        console.log(chalk.gray(`\n  ${notInCube}/${results.length} series not found in CUBE — use pull to retrieve.`));
+    }
+}
+//# sourceMappingURL=cubepath.js.map

package/dist/builtins/net/cubepath.js.map

@@ -0,0 +1 @@
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package/dist/builtins/net/logout.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Logs out from the current ChRIS CUBE session.
+ *
+ * @returns A Promise that resolves when the logout operation is complete.
+ */
+export declare function builtin_logout(): Promise<void>;

package/dist/builtins/net/logout.js

@@ -0,0 +1,24 @@
+/**
+ * @file Builtin logout command.
+ * Disconnects from ChRIS.
+ */
+import chalk from 'chalk';
+import { connect_logout } from '@fnndsc/chili/commands/connect/logout.js';
+import { logout_render } from '@fnndsc/chili/views/connect.js';
+/**
+ * Logs out from the current ChRIS CUBE session.
+ *
+ * @returns A Promise that resolves when the logout operation is complete.
+ */
+export async function builtin_logout() {
+    try {
+        await connect_logout();
+        console.log(logout_render(true));
+    }
+    catch (error) {
+        console.log(logout_render(false));
+        const msg = error instanceof Error ? error.message : String(error);
+        console.error(chalk.red(`Logout failed: ${msg}`));
+    }
+}
+//# sourceMappingURL=logout.js.map

package/dist/builtins/net/logout.js.map

@@ -0,0 +1 @@
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package/dist/builtins/net/pacs.d.ts

@@ -0,0 +1,24 @@
+/**
+ * @file Compound `pacs` command.
+ *
+ * Entry point for all PACS operations: server context management, querying,
+ * and series retrieval. `pacs query` and `pacs pull` delegate to the standalone
+ * builtins, which remain registered as permanent top-level aliases.
+ *
+ * @module
+ */
+/**
+ * PACS subsystem command — server context management, query, and pull.
+ *
+ * Subcommands:
+ *   pacs                      — show active server
+ *   pacs connect              — list servers with active marked
+ *   pacs connect <name|id>    — set active PACS server
+ *   pacs disconnect           — clear active PACS server
+ *   pacs list                 — list servers (alias for: pacs connect)
+ *   pacs query <Key:Value...> — create PACS query and wait for results
+ *   pacs pull <vfs-path...>   — pull DICOM series into ChRIS storage
+ *
+ * @param args - Command arguments (subcommand + its own args).
+ */
+export declare function builtin_pacs(args: string[]): Promise<void>;

package/dist/builtins/net/pacs.js

@@ -0,0 +1,121 @@
+/**
+ * @file Compound `pacs` command.
+ *
+ * Entry point for all PACS operations: server context management, querying,
+ * and series retrieval. `pacs query` and `pacs pull` delegate to the standalone
+ * builtins, which remain registered as permanent top-level aliases.
+ *
+ * @module
+ */
+import chalk from 'chalk';
+import { chrisContext, pacsServers_list } from '@fnndsc/cumin';
+import { builtin_query } from './query.js';
+import { builtin_pull } from '../fs/pull.js';
+import { args_checkHasHelpFlag, help_show } from '../help.js';
+/**
+ * Prints the list of registered PACS servers, marking the active one.
+ *
+ * @param active - Current active PACS server identifier or null.
+ */
+async function servers_print(active) {
+    const result = await pacsServers_list();
+    if (!result.ok || result.value.length === 0) {
+        console.log(chalk.yellow('No PACS servers registered in CUBE.'));
+        return;
+    }
+    console.log('');
+    for (const srv of result.value) {
+        const label = srv.identifier ?? srv.name ?? String(srv.id);
+        const isActive = active !== null &&
+            (label === active || String(srv.id) === active);
+        const marker = isActive ? chalk.green(' ✓ active') : '';
+        const idStr = chalk.gray(`[${srv.id}]`);
+        console.log(`  ${idStr}  ${chalk.cyan(label.padEnd(20))}${marker}`);
+    }
+    console.log('');
+    console.log(chalk.gray('  Use: pacs connect <name|id>'));
+    console.log('');
+}
+/**
+ * PACS subsystem command — server context management, query, and pull.
+ *
+ * Subcommands:
+ *   pacs                      — show active server
+ *   pacs connect              — list servers with active marked
+ *   pacs connect <name|id>    — set active PACS server
+ *   pacs disconnect           — clear active PACS server
+ *   pacs list                 — list servers (alias for: pacs connect)
+ *   pacs query <Key:Value...> — create PACS query and wait for results
+ *   pacs pull <vfs-path...>   — pull DICOM series into ChRIS storage
+ *
+ * @param args - Command arguments (subcommand + its own args).
+ */
+export async function builtin_pacs(args) {
+    if (args_checkHasHelpFlag(args, 'pacs')) {
+        help_show('pacs');
+        return;
+    }
+    const subcommand = args[0];
+    // No subcommand — show active server
+    if (!subcommand) {
+        const active = await chrisContext.PACSserver_get();
+        if (active) {
+            console.log(`Active PACS server: ${chalk.cyan(active)}`);
+            console.log(chalk.gray('  pacs connect         — list all servers'));
+            console.log(chalk.gray('  pacs disconnect      — clear active server'));
+        }
+        else {
+            console.log(chalk.yellow('No PACS server set.'));
+            console.log(chalk.gray('  pacs connect         — list available servers'));
+            console.log(chalk.gray('  pacs connect <id>    — set active server'));
+        }
+        return;
+    }
+    switch (subcommand) {
+        case 'connect': {
+            const target = args[1];
+            if (!target) {
+                const active = await chrisContext.PACSserver_get();
+                await servers_print(active);
+                return;
+            }
+            const ok = await chrisContext.PACSserver_set(target);
+            if (ok) {
+                console.log(chalk.green(`[+] PACS server set to '${target}'`));
+            }
+            else {
+                console.error(chalk.red(`pacs connect: Failed to set server '${target}'`));
+                process.exitCode = 1;
+            }
+            return;
+        }
+        case 'disconnect': {
+            const ok = await chrisContext.PACSserver_set('');
+            if (ok) {
+                console.log(chalk.green('[-] PACS server context cleared.'));
+            }
+            else {
+                console.error(chalk.red('pacs disconnect: Failed to clear PACS server context.'));
+                process.exitCode = 1;
+            }
+            return;
+        }
+        case 'list': {
+            const active = await chrisContext.PACSserver_get();
+            await servers_print(active);
+            return;
+        }
+        case 'query':
+            await builtin_query(args.slice(1));
+            return;
+        case 'pull':
+            await builtin_pull(args.slice(1));
+            return;
+        default:
+            console.error(chalk.red(`pacs: Unknown subcommand '${subcommand}'`));
+            console.log(chalk.gray('  Subcommands: connect, disconnect, list, query, pull'));
+            console.log(chalk.gray('  Try: help pacs'));
+            process.exitCode = 1;
+    }
+}
+//# sourceMappingURL=pacs.js.map

package/dist/builtins/net/pacs.js.map

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package/dist/builtins/net/pacsUtils.d.ts

@@ -0,0 +1,85 @@
+/**
+ * @file Shared PACS utilities for VFS path traversal and CUBE FS resolution.
+ *
+ * Used by `pull` and `cubepath` builtins.
+ *
+ * @module
+ */
+/**
+ * Minimal series info collected from a decoded PACS query result.
+ */
+export interface PACSSeriesInfo {
+    label: string;
+    seriesLabel: string;
+    studyLabel: string;
+    queryLabel: string;
+    seriesUID: string;
+    studyUID: string;
+    pacsName: string;
+    expectedFiles: number;
+}
+/**
+ * CUBE FS resolution result for a single series.
+ */
+export interface SeriesCubePath {
+    folderPath: string;
+    fileCount: number;
+}
+/**
+ * Minimal ChRIS API client slice for PACS series and file queries.
+ */
+export interface ChRISPACSClient {
+    getPACSSeriesList(params: {
+        SeriesInstanceUID: string;
+        limit: number;
+    }, timeout?: number): Promise<{
+        getItems(): Array<unknown>;
+        totalCount: number;
+    }>;
+    getPACSFiles(params: {
+        fname: string;
+        limit: number;
+    }, timeout?: number): Promise<{
+        getItems(): Array<unknown>;
+        totalCount: number;
+    }>;
+}
+/**
+ * Safely unwraps a DICOM tag value (may be `{value: ...}` wrapper or plain string/number).
+ */
+export declare function pacs_tagValueExtract(val: unknown): string;
+/**
+ * Extracts the UID portion of a VFS folder name (`<prefix>_<uid>_<label>`).
+ */
+export declare function folderUID_get(folder: string, prefix: string): string;
+/**
+ * Resolves a PACS server identifier string from a numeric ID or context.
+ *
+ * @param override - Optional numeric-string PACS server ID from flags.
+ * @returns Resolved identifier string, or null if unavailable.
+ */
+export declare function pacsServer_resolve(override?: string | null): Promise<string | null>;
+/**
+ * Walks a `/net/pacs/queries/...` VFS path and collects series info.
+ *
+ * Supports query-level, study-level, and series-level paths.
+ *
+ * @param pathStr - Absolute VFS path to a query, study, or series directory.
+ * @param fallbackPacsName - PACS identifier used when RetrieveAETitle is absent.
+ * @param callerTag - Command name for error messages (e.g. 'pull', 'cubepath').
+ * @returns Array of PACSSeriesInfo for all matched series.
+ */
+export declare function pacs_seriesCollect(pathStr: string, fallbackPacsName: string, callerTag?: string): Promise<PACSSeriesInfo[]>;
+/**
+ * Resolves the CUBE FS folder path and actual file count for a series.
+ *
+ * Retries up to `maxAttempts` times with `retryDelayMs` between attempts
+ * to handle the timing gap between LONK completion and pacsseries DB indexing.
+ *
+ * @param seriesUID - DICOM SeriesInstanceUID.
+ * @param pacsClient - ChRIS API client with getPACSSeriesList and getPACSFiles.
+ * @param maxAttempts - Number of attempts before giving up (default 4).
+ * @param retryDelayMs - Delay between attempts in ms (default 2000).
+ * @returns SeriesCubePath on success, or null if not found.
+ */
+export declare function series_cubePathGet(seriesUID: string, pacsClient: ChRISPACSClient, maxAttempts?: number, retryDelayMs?: number): Promise<SeriesCubePath | null>;