@fnndsc/brasa 0.35.1 → 0.36.0

package/dist/buildinfo.json

@@ -1 +1 @@
-{"hash":"b2d93d"}
+{"hash":"e17e43"}

package/dist/builtins/fs/ls.js

@@ -2,6 +2,7 @@
  * @file Builtin ls command.
  * Lists directory contents.
  */
+import { answerNumbering_of, handle_word, numberedFooter_of } from '../../session/answer.js';
 import chalk from 'chalk';
 import { commandArgs_process, optionsUnknown_refusal, path_resolve } from '../utils.js';
 import { listingCache_get, vfsDispatcher_get } from '../../core/filesystem.js';
@@ -58,6 +59,35 @@ export async function builtin_ls(args) {
         refresh: !!parsed['refresh'] || !!parsed['f'],
     });
 }
+/**
+ * Prefixes each entry line of a long listing with its handle, and adds the
+ * footer. The handles come from the listing's own numbering; when the lines
+ * and the entries do not pair one to one, the listing is left as it was
+ * rather than wearing numbers that could be wrong.
+ *
+ * @param rendered - The long listing as drawn.
+ * @param listings - The entries, per target, in drawn order.
+ * @returns The listing with handles, or as it was.
+ */
+function longHandles_add(rendered, listings) {
+    const handles = answerNumbering_of('fs.listing', listings) ?? [];
+    if (handles.length === 0)
+        return rendered;
+    const lines = rendered.split('\n');
+    const entry = (line) => /^[dl-] /.test(line.replace(/\x1b\[[0-9;]*m/g, ''));
+    if (lines.filter(entry).length !== handles.length)
+        return rendered;
+    const width = Math.max(...handles.map((handle) => handle_word(handle).length));
+    let at = 0;
+    const out = lines.map((line) => {
+        if (!entry(line))
+            return line;
+        const handle = handles[at++];
+        return `${chalk.cyan((handle === undefined ? '' : handle_word(handle)).padEnd(width))}  ${line}`;
+    });
+    const text = out.join('\n');
+    return `${text}${text.endsWith('\n') ? '' : '\n'}${chalk.gray(numberedFooter_of(handles))}\n`;
+}
 /**
  * Whether a path is a folder, as its parent lists it (a mount point counts).
  *
@@ -167,6 +197,11 @@ export async function ls_run(runOptions) {
     if (anyFailed) {
         process.exitCode = 1;
     }
+    // The long form is a table: each entry wears the handle an index expands
+    // to (#1099), and a footer says what is numbered. The short grid stays the
+    // POSIX grid.
+    if (options.long)
+        rendered = longHandles_add(rendered, listings);
     const result = { status: anyFailed ? 'error' : 'ok', rendered };
     result.model = { kind: 'fs.listing', data: listings };
     if (renderedErr.length > 0) {

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

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package/dist/builtins/help.d.ts

@@ -85,6 +85,11 @@ export declare function args_checkHasHelpFlag(args: string[], command?: string):
  * @param args - Command arguments (optional command name).
  */
 export declare function builtin_help(args: string[]): Promise<CommandEnvelope>;
+/**
+ * The groups `help` lists commands under, in order. A command declares its
+ * own (`category` on its help entry); the games shelf is its own page.
+ */
+export declare const HELP_CATEGORIES: ReadonlyArray<string>;
 /**
  * Gets the list of all builtin command names.
  *

package/dist/builtins/help.js

@@ -5,6 +5,7 @@
  *
  * @module
  */
+import { pronounsPage_render } from './pronouns.js';
 import { gamesShelf_render, gamesShelf_names } from './games/shelf.js';
 import chalk from 'chalk';
 import { CAT_USAGE } from './fs/cat.args.js';
@@ -15,6 +16,7 @@ import { backendInstalled_get } from '../core/backend.js';
  */
 export const helpText = {
     sudo: {
+        category: 'Administration',
         usage: 'sudo <command> [arguments...]',
         description: 'Run one ChRIS command with a temporary administrator identity',
         options: [
@@ -27,6 +29,7 @@ export const helpText = {
         ],
     },
     ls: {
+        category: 'Navigation',
         usage: 'ls [options] [path]',
         description: 'List directory contents',
         options: [
@@ -53,6 +56,7 @@ export const helpText = {
         ],
     },
     cd: {
+        category: 'Navigation',
         usage: 'cd [path]',
         description: 'Change current working directory',
         examples: [
@@ -63,8 +67,48 @@ export const helpText = {
             'cd                    # Show current directory',
         ],
     },
+    command: {
+        category: 'General',
+        usage: 'command <name> [args...]',
+        summary: 'Run the system program of a name, not the builtin',
+        description: 'Run the system program of a name, skipping the chell builtin of the same name',
+        options: [
+            'The whole line goes to the host shell as command <name> <args>, reading',
+            'whatever was piped in: query … | command grep -i t1 is plain text grep.',
+            'command -v <name> answers as the host shell does.',
+        ],
+        examples: ['query PatientID:1234567 | command grep -i t1', 'command -v grep'],
+    },
+    grep: {
+        category: 'File Operations',
+        usage: 'grep [-ivwEFc] [-e PATTERN]... [PATTERN]',
+        summary: 'Keep the lines, or the rows of a numbered listing, that match',
+        description: 'Filter text, or a numbered listing keeping its handles',
+        options: [
+            '  -i  ignore case      -v  keep what does not match    -w  whole words',
+            '  -E  extended regex   -F  fixed strings               -c  count only',
+            '  -e PATTERN           a pattern (repeatable: any of them matches)',
+            '',
+            'Fed a numbered listing (piped in, or the held one when nothing is piped),',
+            'grep keeps rows: a matching row stays with the rows above it, a matched',
+            'group keeps all of its rows, and every kept row keeps its handle (@SER41',
+            'stays @SER41). What it kept becomes the listing @ and ${listing} name.',
+            '-c counts and changes nothing.',
+            '',
+            'Text in, or any other flag or a file operand, is the system grep. To skip',
+            'this builtin entirely: command grep …',
+        ],
+        examples: [
+            'query PatientID:1234567,Modality:MR | grep -i t1 | grep -vi gadavist',
+            'grep -i -e t1 -e mprage',
+            'gather list | grep -i sag | gather remove',
+            'cat notes.txt | grep -c todo',
+        ],
+    },
     url: {
+        category: 'Sharing & Tags',
         usage: 'url [path]',
+        summary: 'Print a web address that opens ARGUS at a path, to send to a colleague',
         description: 'Print a web address that opens ARGUS at a path (a feed or node lands in RUNS, anything else in FILES)',
         options: [],
         examples: [
@@ -76,6 +120,7 @@ export const helpText = {
         ],
     },
     pwd: {
+        category: 'Navigation',
         usage: 'pwd [options]',
         description: 'Print current working directory',
         options: [
@@ -94,6 +139,7 @@ export const helpText = {
         ],
     },
     cat: {
+        category: 'File Operations',
         usage: CAT_USAGE,
         description: 'Display file contents, with terminal syntax highlighting for recognized text formats',
         options: [
@@ -111,6 +157,7 @@ export const helpText = {
         ],
     },
     rm: {
+        category: 'File Operations',
         usage: 'rm [options] <path> [path...]',
         description: 'Remove files or directories',
         options: [
@@ -134,6 +181,7 @@ export const helpText = {
         ],
     },
     cp: {
+        category: 'File Operations',
         usage: 'cp [-t <dir>] [options] <source...> [dest]',
         description: 'Copy files or directories (supports wildcards and multiple sources)',
         options: [
@@ -159,6 +207,7 @@ export const helpText = {
         ],
     },
     mv: {
+        category: 'File Operations',
         usage: 'mv [-t <dir>] <source...> [dest]',
         description: 'Move or rename files or directories (supports wildcards and multiple sources)',
         options: [
@@ -174,6 +223,7 @@ export const helpText = {
         ],
     },
     touch: {
+        category: 'File Operations',
         usage: 'touch [options] <file>',
         description: 'Create empty files or files with content',
         options: [
@@ -187,6 +237,7 @@ export const helpText = {
         ],
     },
     mkdir: {
+        category: 'File Operations',
         usage: 'mkdir [-p] <directory> [directory...]',
         description: 'Create directories',
         options: [
@@ -201,6 +252,7 @@ export const helpText = {
         ],
     },
     rmdir: {
+        category: 'File Operations',
         usage: 'rmdir <directory> [directory...]',
         summary: 'Remove empty directories',
         description: 'Removes each folder only when it is empty, as on Linux: one that holds anything is '
@@ -211,16 +263,19 @@ export const helpText = {
         ],
     },
     exit: {
+        category: 'General',
         usage: 'exit',
         description: 'Exit the shell',
         examples: ['exit'],
     },
     version: {
+        category: 'General',
         usage: 'version',
         description: 'Report the versions of the mise stack layers running this session',
         examples: ['version'],
     },
     fortune: {
+        category: 'Games and utilities',
         usage: 'fortune',
         summary: 'Print a random fortune cookie',
         description: 'Prints a random fortune — the classic UNIX fortune cookie, bundled and self-contained.',
@@ -460,12 +515,14 @@ export const helpText = {
         examples: ['2048'],
     },
     notes: {
+        category: 'General',
         usage: 'notes [--since N|YYYY-MM-DD] [--all] [--long]',
         summary: 'What the installed releases changed, for the operator',
         description: 'Reads the release notes shipped with the packages installed where this session runs — argus, brasa, chell, calypso, porter — and lists the newest release: one row per change, the package tagged. --since N shows the last N releases, --since DATE everything from a day on; --long unfolds each change beneath its first sentence; --all includes the changes marked Internal. help notes is the same. In ARGUS the WHAT\'S NEW block opens them as a listing.',
         examples: ['notes', 'notes --since 3', 'notes --since 2026-10-01 --long', 'notes --all'],
     },
     weather: {
+        category: 'Games and utilities',
         usage: 'weather [place] [-u|--units metric|imperial] [-d|--days N]',
         summary: 'The weather at a place, now and the next few days',
         description: 'Reports the current conditions and a short forecast for a place, from Open-Meteo (no key, no account). The place is found by name; with none given it is Boston. Metric (°C, km/h) unless --units imperial asks for °F and mph. The call is made from the session host, so it needs that host to reach the internet.',
@@ -476,6 +533,7 @@ export const helpText = {
         examples: ['weather', 'weather Cape Town', 'weather Boston --units imperial', 'weather Paris -d 7'],
     },
     date: {
+        category: 'General',
         usage: 'date [-u] [+FORMAT]',
         summary: 'Print the current date and time',
         description: 'Prints the current date and time, in the spirit of UNIX date. Use -u for UTC and +FORMAT for a strftime-style format string. Reports the time only; it never sets the clock.',
@@ -486,12 +544,14 @@ export const helpText = {
         examples: ['date', 'date -u', 'date +%Y-%m-%d', 'date "+%A, %B %e %Y"'],
     },
     cal: {
+        category: 'Games and utilities',
         usage: 'cal [[month] year]',
         summary: 'Print a calendar',
         description: 'Prints a month or year calendar with today highlighted, in the spirit of UNIX cal.',
         examples: ['cal', 'cal 2026', 'cal 7 2026'],
     },
     prompt: {
+        category: 'Shell Settings',
         usage: 'prompt [list | <theme>]',
         description: 'List available prompt themes or switch the active theme',
         options: [
@@ -506,6 +566,7 @@ export const helpText = {
         ],
     },
     timing: {
+        category: 'Shell Settings',
         usage: 'timing [on|off]',
         description: 'Toggle or display command timing mode',
         options: [
@@ -519,6 +580,7 @@ export const helpText = {
         ],
     },
     debug: {
+        category: 'Shell Settings',
         usage: 'debug [on|off]',
         description: 'Toggle or display debug mode (verbose logging)',
         options: [
@@ -532,6 +594,7 @@ export const helpText = {
         ],
     },
     help: {
+        category: 'General',
         usage: 'help [command]',
         description: 'Display help information',
         examples: [
@@ -542,6 +605,7 @@ export const helpText = {
         ],
     },
     '!': {
+        category: 'General',
         usage: '! <shell_command>',
         description: 'Execute command on host shell (shell escape)',
         examples: [
@@ -817,6 +881,11 @@ export function args_checkHasHelpFlag(args, command) {
  */
 export async function builtin_help(args) {
     const commandName = args.length > 0 ? args.join(' ') : undefined;
+    // The pronouns: the core's page, with whatever the backend answers too.
+    if (commandName === 'pronouns') {
+        const backendPage = (await backendInstalled_get()?.fallback?.help?.('pronouns')) ?? null;
+        return { status: 'ok', rendered: backendPage ?? pronounsPage_render([]) };
+    }
     // The shelf: its own page, in the style of this one.
     if (commandName === 'games') {
         return { status: 'ok', rendered: gamesShelf_render(commandSummary_get) };
@@ -844,22 +913,13 @@ export async function builtin_help(args) {
     rendered += `${chalk.bold.cyan('ChELL - Available Commands')}\n`;
     rendered += `${chalk.gray('─'.repeat(60))}\n`;
     rendered += '\n';
-    // Group commands by category
-    const categories = {
-        Navigation: ['cd', 'pwd', 'ls', 'tree', 'du'],
-        'File Operations': ['cat', 'edit', 'cp', 'mv', 'rm', 'touch', 'mkdir', 'rmdir', 'upload', 'download'],
-        'Sharing & Tags': ['setfacl', 'getfacl', 'chmod', 'getfattr', 'setfattr'],
-        Connection: ['connect', 'logout', 'context', 'id', 'whoami', 'whereami', 'netstat'],
-        Monitoring: ['proc'],
-        Imaging: ['dcm', 'image'],
-        'Single Resource': ['plugin', 'pipeline', 'feed', 'tag', 'group', 'pluginmeta', 'plugininstance', 'workflow'],
-        'Resource Collections': ['plugins', 'feeds', 'files', 'links', 'dirs', 'store', 'compute', 'tags', 'groups', 'pluginmetas', 'plugininstances', 'workflows', 'parametersofplugin'],
-        PACS: ['pacs', 'pacsservers', 'pacsqueries', 'pacsretrieve'],
-        Administration: ['sudo', 'user'],
-        'Shell Settings': ['physicalmode', 'prompt', 'timing', 'debug'],
-        'Games and utilities': ['fortune', 'cal', 'weather', 'motd'],
-        General: ['help', 'notes', 'date', 'exit', '!'],
-    };
+    // Group commands by the category each declares (HELP_CATEGORIES order).
+    const categories = Object.fromEntries(HELP_CATEGORIES.map((category) => [category, []]));
+    for (const name of helpTopic_names()) {
+        const category = commandHelpEntry_get(name)?.category;
+        if (category !== undefined && name.indexOf(' ') < 0)
+            (categories[category] ??= []).push(name);
+    }
     // Display commands by category
     for (const [category, commands] of Object.entries(categories)) {
         const runnable = commands.filter((cmd) => verb_available(cmd) && commandHelpEntry_get(cmd) !== undefined);
@@ -882,15 +942,28 @@ export async function builtin_help(args) {
     }
     // Display Shell Features
     rendered += `${chalk.bold.yellow('Shell Features')}\n`;
-    rendered += `  ${chalk.cyan('Pipes'.padEnd(20))} ${chalk.gray('Chain commands: cat file.txt | wc -l')}\n`;
+    rendered += `  ${chalk.cyan('Pipes'.padEnd(20))} ${chalk.gray('Chain commands: cat file.txt | wc -l; a numbered listing travels to the next builtin: query … | gather add')}\n`;
     rendered += `  ${chalk.cyan('Redirection >'.padEnd(20))} ${chalk.gray('Write to file: cat file.txt > output.txt')}\n`;
     rendered += `  ${chalk.cyan('Redirection >>'.padEnd(20))} ${chalk.gray('Append to file: cat file.txt >> output.txt')}\n`;
+    rendered += `  ${chalk.cyan('Listing-aware grep'.padEnd(20))} ${chalk.gray('Filter a numbered listing, keeping its handles: … | grep -i t1 (help grep)')}\n`;
+    rendered += `  ${chalk.cyan('command'.padEnd(20))} ${chalk.gray('Run the system program, not the builtin: … | command grep -i t1')}\n`;
+    rendered += `  ${chalk.cyan('Index handles'.padEnd(20))} ${chalk.gray('Name rows of the last numbered listing: gather add @SER3  @SER1-4  @SER2,5,7')}\n`;
+    rendered += `  ${chalk.cyan('Pronouns ${…}'.padEnd(20))} ${chalk.gray('What this session just made or asked, as ${name}: ${cwd} … (help pronouns)')}\n`;
     rendered += '\n';
     rendered += `${chalk.gray('Type "help <command>" for detailed information about a command.')}\n`;
     rendered += `${chalk.gray('Type "<command> --help" for quick help on any command.')}\n`;
     rendered += '\n';
     return { status: 'ok', rendered };
 }
+/**
+ * The groups `help` lists commands under, in order. A command declares its
+ * own (`category` on its help entry); the games shelf is its own page.
+ */
+export const HELP_CATEGORIES = [
+    'Navigation', 'File Operations', 'Sharing & Tags', 'Connection', 'Monitoring', 'Imaging',
+    'Workflows & Cohorts', 'Single Resource', 'Resource Collections', 'PACS', 'Administration',
+    'Shell Settings', 'Games and utilities', 'General',
+];
 /**
  * Gets the list of all builtin command names.
  *

package/dist/builtins/help.js.map

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package/dist/builtins/net/query.csv.d.ts

@@ -1,21 +1,3 @@
-/**
- * @file A PACS answer as a table a spreadsheet can read.
- *
- * There has been a `--csv` on listings since chili, and it renders the same
- * way this does — headers uppercased, every cell quoted, embedded quotes
- * doubled — but it renders it inside a chili handler rather than from a
- * function anything else can call. Rather than grow a dependency on a
- * package the stack is trying to shed, the rule is stated here, once, and
- * the PACS answer is the first thing to use it.
- *
- * The shape is settled by doctrine rather than by convenience: a row per
- * STUDY (or, asked with `--series`, per series), and a row for every
- * patient that owns none. The MRNs that come
- * back are the ones with imaging, so a table built from studies alone
- * would quietly drop exactly the rows an audit is asking about.
- *
- * @module
- */
 import type { PacsQueryModel } from '@fnndsc/menu';
 /**
  * How far down an answer's rows go: one per STUDY (the audit's grain, and
@@ -38,6 +20,7 @@ export type PacsAnswerLevel = 'study' | 'series';
 export declare function pacsAnswer_rows(model: PacsQueryModel, level?: PacsAnswerLevel): {
     columns: ReadonlyArray<string>;
     rows: string[][];
+    keys: Array<string | null>;
 };
 /**
  * Renders one answer as CSV.

package/dist/builtins/net/query.csv.js

@@ -1,3 +1,22 @@
+/**
+ * @file A PACS answer as a table a spreadsheet can read.
+ *
+ * There has been a `--csv` on listings since chili, and it renders the same
+ * way this does — headers uppercased, every cell quoted, embedded quotes
+ * doubled — but it renders it inside a chili handler rather than from a
+ * function anything else can call. Rather than grow a dependency on a
+ * package the stack is trying to shed, the rule is stated here, once, and
+ * the PACS answer is the first thing to use it.
+ *
+ * The shape is settled by doctrine rather than by convenience: a row per
+ * STUDY (or, asked with `--series`, per series), and a row for every
+ * patient that owns none. The MRNs that come
+ * back are the ones with imaging, so a table built from studies alone
+ * would quietly drop exactly the rows an audit is asking about.
+ *
+ * @module
+ */
+import { answerNumbering_of, handleWords_of, numberedFooter_of } from '../../session/answer.js';
 /** The columns of a study-level table, in reading order. */
 const STUDY_COLUMNS = [
     'MRN', 'PATIENT', 'SERVER', 'STATUS', 'STUDY', 'DATE',
@@ -40,19 +59,27 @@ function cell_quote(value) {
  */
 export function pacsAnswer_rows(model, level = 'study') {
     const rows = [];
+    // What each row is, for the handle a screen prints beside it (`STD:<path>`,
+    // `SER:<path>`); null for a row nothing numbers. Never in the CSV.
+    const keys = [];
     const patients = model.patients ?? [];
     const studiesOf = (patient) => model.studies.filter((study) => study.patientId === patient.patientId
         && (patient.server === undefined || study.server === undefined || study.server === patient.server));
     const study_rows = (study, facts) => {
         if (level === 'study') {
+            keys.push(study.vfsPath === undefined ? null : `STD:${study.vfsPath}`);
             return [[
                     facts.mrn, study.patientName, facts.server, facts.status, study.description, study.date,
                     study.accession, study.modalities, String(study.series.length), facts.answeredAt,
                 ]];
         }
         const lead = [facts.mrn, study.patientName, facts.server, facts.status, study.description, study.date, study.accession];
-        if (study.series.length === 0)
+        if (study.series.length === 0) {
+            keys.push(null);
             return [[...lead, '', '', '', '', '', facts.answeredAt]];
+        }
+        for (const series of study.series)
+            keys.push(series.vfsPath === undefined ? null : `SER:${series.vfsPath}`);
         return study.series.map((series, index) => [
             ...lead,
             String(index + 1),
@@ -76,6 +103,7 @@ export function pacsAnswer_rows(model, level = 'study') {
                 // audit is usually about: a patient with no imaging, or one whose
                 // question could not be asked at all.
                 rows.push(patient_row(patient, server, answeredAt));
+                keys.push(null);
                 continue;
             }
             for (const study of owned) {
@@ -93,7 +121,7 @@ export function pacsAnswer_rows(model, level = 'study') {
             }));
         }
     }
-    return { columns: level === 'study' ? STUDY_COLUMNS : SERIES_COLUMNS, rows };
+    return { columns: level === 'study' ? STUDY_COLUMNS : SERIES_COLUMNS, rows, keys };
 }
 /**
  * Renders one answer as CSV.
@@ -125,7 +153,16 @@ export function pacsAnswer_toCsv(model, level = 'study') {
  * @returns The table, header and rule first, uncoloured.
  */
 export function pacsAnswer_toTable(model, level = 'study') {
-    const { columns, rows } = pacsAnswer_rows(model, level);
+    const table = pacsAnswer_rows(model, level);
+    // The handle each row answers to leads the screen's table (#1099); the
+    // CSV, a record of the answer, does not carry it.
+    const numbered = answerNumbering_of('pacs.query', model) ?? [];
+    const words = handleWords_of(numbered);
+    // A column is earned: an answer nothing numbers (no paths yet) keeps the
+    // table it always had.
+    const lead = table.keys.some((key) => key !== null && words.has(key));
+    const columns = lead ? ['@', ...table.columns] : table.columns;
+    const rows = lead ? table.rows.map((row, at) => [words.get(table.keys[at] ?? '') ?? '', ...row]) : table.rows;
     const shown = columns.map((_, index) => index).filter((index) => columns[index] !== 'ANSWERED');
     const widths = shown.map((index) => Math.max(columns[index]?.length ?? 0, ...rows.map((row) => (row[index] ?? '').length)));
     const line = (cells) => `  ${shown.map((index, at) => (cells[index] ?? '').padEnd(widths[at] ?? 0)).join('  ').trimEnd()}`;
@@ -133,6 +170,9 @@ export function pacsAnswer_toTable(model, level = 'study') {
     for (const row of rows)
         out.push(line(row));
     out.push('', `  ${rows.length} row${rows.length === 1 ? '' : 's'}, one per ${level}`);
+    const footer = numberedFooter_of(numbered);
+    if (footer !== '')
+        out.push(`  ${footer}`);
     return `${out.join('\n')}\n`;
 }
 /**