@fnndsc/brasa 0.55.2 → 0.56.0

package/dist/builtins/berth/berthState.d.ts

@@ -0,0 +1,139 @@
+/** The environment variable naming a berth's anchors folder. */
+export declare const BERTH_ANCHORS_ENV: string;
+/** The environment variable naming a berth's outgoing folder. */
+export declare const BERTH_OUTGOING_ENV: string;
+/** The state file's name, inside the anchors folder. */
+export declare const BERTH_STATE_FILE: string;
+/**
+ * The two places of a berth.
+ *
+ * @example
+ * ```ts
+ * const places: BerthPlaces = { anchors: '/anchors', outgoing: '/outgoing' };
+ * ```
+ */
+export interface BerthPlaces {
+    /** The folder each anchor is downloaded into, one folder per anchor. */
+    readonly anchors: string;
+    /** The folder the person's work is returned from. */
+    readonly outgoing: string;
+}
+/**
+ * One file an anchor downloaded.
+ *
+ * @example
+ * ```ts
+ * const file: AnchoredFile = { name: 'anat/t1.nii', size: 1024 };
+ * ```
+ */
+export interface AnchoredFile {
+    /** Its name relative to the anchor's folder, with `/` between parts. */
+    readonly name: string;
+    /** Its size in bytes, as ChRIS gave it. */
+    readonly size: number;
+}
+/**
+ * One anchor: a ChRIS path downloaded into the berth.
+ *
+ * @example
+ * ```ts
+ * const anchor: BerthAnchor = {
+ *   name: 'sub-01', path: '/home/alice/feeds/feed_5/pl-dircopy_7/data/sub-01',
+ *   node: 7, feed: 5, files: [{ name: 't1.nii', size: 1024 }], anchoredAt: '2026-11-13T10:00:00.000Z',
+ * };
+ * ```
+ */
+export interface BerthAnchor {
+    /** Its name: the folder under the anchors place. */
+    readonly name: string;
+    /** The ChRIS path it was downloaded from, absolute. */
+    readonly path: string;
+    /** The plugin instance the path runs through, under the person's own feeds; null anywhere else. */
+    readonly node: number | null;
+    /** The feed of that node; null when there is no node. */
+    readonly feed: number | null;
+    /** Every file downloaded, for the close's check of a changed input. */
+    readonly files: readonly AnchoredFile[];
+    /** When it was downloaded. */
+    readonly anchoredAt: string;
+}
+/**
+ * A berth's state, as the state file holds it.
+ *
+ * @example
+ * ```ts
+ * const state: BerthState = { version: 1, anchors: [], lastClosedAt: null };
+ * ```
+ */
+export interface BerthState {
+    /** The file's format version. */
+    readonly version: number;
+    /** The anchors, in the order they were made. */
+    readonly anchors: readonly BerthAnchor[];
+    /** When the berth last closed; null when it never has. */
+    readonly lastClosedAt: string | null;
+}
+/** A state file that cannot be read as a berth's state. */
+export declare class BerthStateError extends Error {
+    /**
+     * @param file - The state file.
+     * @param why - What is wrong with it.
+     */
+    constructor(file: string, why: string);
+}
+/**
+ * The places of the berth this session runs in.
+ *
+ * @param env - The environment to read; the process's by default.
+ * @returns Both places, or null when either is unset (the session runs on a host).
+ *
+ * @example
+ * ```ts
+ * berthPlaces_read({ MISE_BERTH_ANCHORS: '/anchors', MISE_BERTH_OUTGOING: '/outgoing' }); // { anchors: '/anchors', outgoing: '/outgoing' }
+ * berthPlaces_read({}); // null
+ * ```
+ */
+export declare function berthPlaces_read(env?: NodeJS.ProcessEnv): BerthPlaces | null;
+/**
+ * Reads a berth's state file.
+ *
+ * @param anchorsDir - The berth's anchors folder.
+ * @returns The state; the empty state when there is no file yet.
+ * @throws {BerthStateError} When the file is there but is not a berth's state.
+ *
+ * @example
+ * ```ts
+ * const state: BerthState = berthState_read('/anchors');
+ * state.anchors.map((anchor: BerthAnchor): string => anchor.name); // ['sub-01']
+ * ```
+ */
+export declare function berthState_read(anchorsDir: string): BerthState;
+/**
+ * Writes a berth's state file whole: to a temporary file beside it, then
+ * renamed over it, so a reader sees the old state or the new and never part.
+ *
+ * @param anchorsDir - The berth's anchors folder.
+ * @param state - The state to write.
+ *
+ * @example
+ * ```ts
+ * berthState_write('/anchors', { version: 1, anchors: [], lastClosedAt: '2026-11-13T12:00:00.000Z' });
+ * ```
+ */
+export declare function berthState_write(anchorsDir: string, state: BerthState): void;
+/**
+ * Reads the state, changes it and writes it, with nothing between the read
+ * and the write: the steps are synchronous, so two lines of one session that
+ * change the state never lose each other's change.
+ *
+ * @param anchorsDir - The berth's anchors folder.
+ * @param change - The change: the state as read, to the state to write.
+ * @returns The state written.
+ * @throws {BerthStateError} When the file there is not a berth's state.
+ *
+ * @example
+ * ```ts
+ * berthState_update('/anchors', (state: BerthState): BerthState => ({ ...state, anchors: [] }));
+ * ```
+ */
+export declare function berthState_update(anchorsDir: string, change: (state: BerthState) => BerthState): BerthState;

package/dist/builtins/berth/berthState.js

@@ -0,0 +1,194 @@
+/**
+ * @file A berth's places and its state file: where anchors and outgoing work
+ * live, and what has been anchored there.
+ *
+ * A berth container names its two places in the environment:
+ * `MISE_BERTH_ANCHORS` (where each anchor is downloaded, `/anchors`) and
+ * `MISE_BERTH_OUTGOING` (the person's work to return, `/outgoing`). A session
+ * without them runs on a host, not in a berth. The state is one JSON file in
+ * the anchors place, `.berth.json`: every anchor with its ChRIS path, its node
+ * and feed (or none), the files downloaded with their sizes, when it was
+ * anchored, and when the berth last closed. It is written whole, to a
+ * temporary file renamed over the old one, so a reader never sees half of it.
+ *
+ * Key components:
+ * - BerthPlaces: the anchors and outgoing folders of a berth.
+ * - BerthState, BerthAnchor, AnchoredFile: the state file's shape.
+ * - berthPlaces_read: the places from the environment, or null on a host.
+ * - berthState_read / berthState_write: read and write the state file.
+ * - berthState_update: read, change and write the state in one step.
+ *
+ * Typical usage:
+ * ```ts
+ * const places: BerthPlaces | null = berthPlaces_read();
+ * if (places !== null) {
+ *   const state: BerthState = berthState_read(places.anchors);
+ *   berthState_update(places.anchors, (now: BerthState): BerthState => ({ ...now, lastClosedAt: new Date().toISOString() }));
+ * }
+ * ```
+ *
+ * Dependencies: Node.js built-ins only. Times are ISO 8601 strings.
+ *
+ * @module
+ */
+import { existsSync, readFileSync, renameSync, writeFileSync } from 'node:fs';
+import { join } from 'node:path';
+/** The environment variable naming a berth's anchors folder. */
+export const BERTH_ANCHORS_ENV = 'MISE_BERTH_ANCHORS';
+/** The environment variable naming a berth's outgoing folder. */
+export const BERTH_OUTGOING_ENV = 'MISE_BERTH_OUTGOING';
+/** The state file's name, inside the anchors folder. */
+export const BERTH_STATE_FILE = '.berth.json';
+/** The state file's format version. */
+const BERTH_STATE_VERSION = 1;
+/** A state file that cannot be read as a berth's state. */
+export class BerthStateError extends Error {
+    /**
+     * @param file - The state file.
+     * @param why - What is wrong with it.
+     */
+    constructor(file, why) {
+        super(`${file}: ${why}`);
+        this.name = 'BerthStateError';
+    }
+}
+/**
+ * The places of the berth this session runs in.
+ *
+ * @param env - The environment to read; the process's by default.
+ * @returns Both places, or null when either is unset (the session runs on a host).
+ *
+ * @example
+ * ```ts
+ * berthPlaces_read({ MISE_BERTH_ANCHORS: '/anchors', MISE_BERTH_OUTGOING: '/outgoing' }); // { anchors: '/anchors', outgoing: '/outgoing' }
+ * berthPlaces_read({}); // null
+ * ```
+ */
+export function berthPlaces_read(env = process.env) {
+    const anchors = env[BERTH_ANCHORS_ENV];
+    const outgoing = env[BERTH_OUTGOING_ENV];
+    if (anchors === undefined || anchors === '' || outgoing === undefined || outgoing === '')
+        return null;
+    return { anchors, outgoing };
+}
+/**
+ * A state with nothing in it: no anchor, never closed.
+ *
+ * @returns The empty state.
+ */
+function berthState_empty() {
+    return { version: BERTH_STATE_VERSION, anchors: [], lastClosedAt: null };
+}
+/**
+ * Reads one anchored file from the state file's JSON.
+ *
+ * @param raw - The parsed value.
+ * @param file - The state file, for the error.
+ * @returns The file.
+ * @throws {BerthStateError} When it is not a file entry.
+ */
+function anchoredFile_parse(raw, file) {
+    const entry = (typeof raw === 'object' && raw !== null ? raw : {});
+    if (typeof entry['name'] !== 'string' || typeof entry['size'] !== 'number')
+        throw new BerthStateError(file, 'a file entry wants a name and a size');
+    return { name: entry['name'], size: entry['size'] };
+}
+/**
+ * Reads one anchor from the state file's JSON.
+ *
+ * @param raw - The parsed value.
+ * @param file - The state file, for the error.
+ * @returns The anchor.
+ * @throws {BerthStateError} When it is not an anchor entry.
+ */
+function berthAnchor_parse(raw, file) {
+    const entry = (typeof raw === 'object' && raw !== null ? raw : {});
+    const node = entry['node'];
+    const feed = entry['feed'];
+    if (typeof entry['name'] !== 'string' || typeof entry['path'] !== 'string' || typeof entry['anchoredAt'] !== 'string'
+        || !(node === null || typeof node === 'number') || !(feed === null || typeof feed === 'number') || !Array.isArray(entry['files'])) {
+        throw new BerthStateError(file, 'an anchor wants a name, a path, a node, a feed, files and anchoredAt');
+    }
+    return {
+        name: entry['name'],
+        path: entry['path'],
+        node,
+        feed,
+        files: entry['files'].map((one) => anchoredFile_parse(one, file)),
+        anchoredAt: entry['anchoredAt'],
+    };
+}
+/**
+ * Reads a berth's state file.
+ *
+ * @param anchorsDir - The berth's anchors folder.
+ * @returns The state; the empty state when there is no file yet.
+ * @throws {BerthStateError} When the file is there but is not a berth's state.
+ *
+ * @example
+ * ```ts
+ * const state: BerthState = berthState_read('/anchors');
+ * state.anchors.map((anchor: BerthAnchor): string => anchor.name); // ['sub-01']
+ * ```
+ */
+export function berthState_read(anchorsDir) {
+    const file = join(anchorsDir, BERTH_STATE_FILE);
+    if (!existsSync(file))
+        return berthState_empty();
+    let parsed;
+    try {
+        parsed = JSON.parse(readFileSync(file, 'utf8'));
+    }
+    catch (error) {
+        throw new BerthStateError(file, error instanceof Error ? error.message : String(error));
+    }
+    const raw = (typeof parsed === 'object' && parsed !== null ? parsed : {});
+    const closed = raw['lastClosedAt'];
+    if (!Array.isArray(raw['anchors']) || !(closed === null || closed === undefined || typeof closed === 'string')) {
+        throw new BerthStateError(file, 'not a berth state (anchors, lastClosedAt)');
+    }
+    return {
+        version: typeof raw['version'] === 'number' ? raw['version'] : BERTH_STATE_VERSION,
+        anchors: raw['anchors'].map((one) => berthAnchor_parse(one, file)),
+        lastClosedAt: closed ?? null,
+    };
+}
+/**
+ * Writes a berth's state file whole: to a temporary file beside it, then
+ * renamed over it, so a reader sees the old state or the new and never part.
+ *
+ * @param anchorsDir - The berth's anchors folder.
+ * @param state - The state to write.
+ *
+ * @example
+ * ```ts
+ * berthState_write('/anchors', { version: 1, anchors: [], lastClosedAt: '2026-11-13T12:00:00.000Z' });
+ * ```
+ */
+export function berthState_write(anchorsDir, state) {
+    const file = join(anchorsDir, BERTH_STATE_FILE);
+    const temporary = `${file}.${process.pid}.tmp`;
+    writeFileSync(temporary, `${JSON.stringify({ ...state, version: BERTH_STATE_VERSION }, null, 2)}\n`, { mode: 0o644 });
+    renameSync(temporary, file);
+}
+/**
+ * Reads the state, changes it and writes it, with nothing between the read
+ * and the write: the steps are synchronous, so two lines of one session that
+ * change the state never lose each other's change.
+ *
+ * @param anchorsDir - The berth's anchors folder.
+ * @param change - The change: the state as read, to the state to write.
+ * @returns The state written.
+ * @throws {BerthStateError} When the file there is not a berth's state.
+ *
+ * @example
+ * ```ts
+ * berthState_update('/anchors', (state: BerthState): BerthState => ({ ...state, anchors: [] }));
+ * ```
+ */
+export function berthState_update(anchorsDir, change) {
+    const next = change(berthState_read(anchorsDir));
+    berthState_write(anchorsDir, next);
+    return next;
+}
+//# sourceMappingURL=berthState.js.map

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package/dist/builtins/berth/berthWords.d.ts

@@ -0,0 +1,87 @@
+/**
+ * @file The words the `berth` subcommands share: a refusal in the verb's
+ * tone, a count with its noun, the bytes of some files, and an anchor's node
+ * as the listing names it.
+ *
+ * Key components:
+ * - BerthRefusal: a refusal, said after `berth: ` with an exit status of 1.
+ * - count_say: `1 file`, `3 files`.
+ * - columns_render: rows laid out in columns.
+ * - bytes_sum: the sum of some files' sizes.
+ * - anchorNode_show: an anchor's node by its folder name, or `none`.
+ *
+ * Typical usage:
+ * ```ts
+ * throw new BerthRefusal(`close: ${count_say(2, 'anchor')} have no node`);
+ * ```
+ *
+ * Dependencies: none.
+ *
+ * @module
+ */
+import type { BerthAnchor } from './berthState.js';
+/**
+ * A refusal: the verb's words for it, and an exit status of 1.
+ *
+ * @example
+ * ```ts
+ * throw new BerthRefusal('drop: no anchor named sub-01');
+ * ```
+ */
+export declare class BerthRefusal extends Error {
+    /**
+     * @param message - The words after `berth: `.
+     */
+    constructor(message: string);
+}
+/**
+ * A count with its noun, `1 file`, `3 files`.
+ *
+ * @param count - The count.
+ * @param noun - The noun, singular.
+ * @returns The words.
+ *
+ * @example
+ * ```ts
+ * count_say(3, 'file'); // '3 files'
+ * ```
+ */
+export declare function count_say(count: number, noun: string): string;
+/**
+ * The sum of the sizes of some files.
+ *
+ * @param files - The files.
+ * @returns Their bytes.
+ *
+ * @example
+ * ```ts
+ * bytes_sum([{ size: 4 }, { size: 6 }]); // 10
+ * ```
+ */
+export declare function bytes_sum(files: ReadonlyArray<{
+    readonly size: number;
+}>): number;
+/**
+ * Lays rows out in columns, each as wide as its widest cell.
+ *
+ * @param rows - The rows, the header first.
+ * @returns The lines.
+ *
+ * @example
+ * ```ts
+ * columns_render([['PID', 'COMMAND'], ['412', 'vim']]); // ['PID  COMMAND', '412  vim']
+ * ```
+ */
+export declare function columns_render(rows: readonly (readonly string[])[]): string[];
+/**
+ * The node of an anchor by its folder name, read from its path.
+ *
+ * @param anchor - The anchor.
+ * @returns `pl-fshack_41`, the id when the path names no such folder, or `none`.
+ *
+ * @example
+ * ```ts
+ * anchorNode_show({ name: 'sub-01', path: '/home/alice/feeds/feed_5/pl-fshack_41/data/sub-01', node: 41, feed: 5, files: [], anchoredAt: '' }); // 'pl-fshack_41'
+ * ```
+ */
+export declare function anchorNode_show(anchor: BerthAnchor): string;

package/dist/builtins/berth/berthWords.js

@@ -0,0 +1,78 @@
+/**
+ * A refusal: the verb's words for it, and an exit status of 1.
+ *
+ * @example
+ * ```ts
+ * throw new BerthRefusal('drop: no anchor named sub-01');
+ * ```
+ */
+export class BerthRefusal extends Error {
+    /**
+     * @param message - The words after `berth: `.
+     */
+    constructor(message) {
+        super(message);
+        this.name = 'BerthRefusal';
+    }
+}
+/**
+ * A count with its noun, `1 file`, `3 files`.
+ *
+ * @param count - The count.
+ * @param noun - The noun, singular.
+ * @returns The words.
+ *
+ * @example
+ * ```ts
+ * count_say(3, 'file'); // '3 files'
+ * ```
+ */
+export function count_say(count, noun) {
+    return `${count} ${noun}${count === 1 ? '' : 's'}`;
+}
+/**
+ * The sum of the sizes of some files.
+ *
+ * @param files - The files.
+ * @returns Their bytes.
+ *
+ * @example
+ * ```ts
+ * bytes_sum([{ size: 4 }, { size: 6 }]); // 10
+ * ```
+ */
+export function bytes_sum(files) {
+    return files.reduce((total, file) => total + file.size, 0);
+}
+/**
+ * Lays rows out in columns, each as wide as its widest cell.
+ *
+ * @param rows - The rows, the header first.
+ * @returns The lines.
+ *
+ * @example
+ * ```ts
+ * columns_render([['PID', 'COMMAND'], ['412', 'vim']]); // ['PID  COMMAND', '412  vim']
+ * ```
+ */
+export function columns_render(rows) {
+    const widths = (rows[0] ?? []).map((_cell, at) => Math.max(...rows.map((row) => (row[at] ?? '').length)));
+    return rows.map((row) => row.map((cell, at) => (at === row.length - 1 ? cell : cell.padEnd(widths[at] ?? 0))).join('  ').trimEnd());
+}
+/**
+ * The node of an anchor by its folder name, read from its path.
+ *
+ * @param anchor - The anchor.
+ * @returns `pl-fshack_41`, the id when the path names no such folder, or `none`.
+ *
+ * @example
+ * ```ts
+ * anchorNode_show({ name: 'sub-01', path: '/home/alice/feeds/feed_5/pl-fshack_41/data/sub-01', node: 41, feed: 5, files: [], anchoredAt: '' }); // 'pl-fshack_41'
+ * ```
+ */
+export function anchorNode_show(anchor) {
+    if (anchor.node === null)
+        return 'none';
+    return anchor.path.split('/').reverse().find((segment) => segment.endsWith(`_${anchor.node}`)) ?? String(anchor.node);
+}
+//# sourceMappingURL=berthWords.js.map

package/dist/builtins/berth/berthWords.js.map

@@ -0,0 +1 @@
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package/dist/builtins/helpSections.js

@@ -20,7 +20,7 @@ export const HELP_SECTIONS = [
     { name: 'Connection', blurb: 'Who you are, which CUBE you are on, and where the session stands.', examples: ['connect', 'whoami', 'context'] },
     { name: 'Monitoring', blurb: 'Live jobs as a filesystem, and jumping to one by number.', examples: ['proc'] },
     { name: 'Imaging', blurb: 'DICOM tags and image viewing.', examples: ['dcm', 'image'] },
-    { name: 'Workflows', blurb: 'Gather a cohort, record what you do as a manifest, and replay it.', examples: ['gather', 'record', 'play', 'expect'] },
+    { name: 'Workflows', blurb: 'Gather a cohort, anchor ChRIS paths in a berth, record what you do as a manifest, and replay it.', examples: ['gather', 'berth', 'record', 'play', 'expect'] },
     { name: 'Resources', blurb: 'ChRIS resources one at a time or as lists: feeds, plugins, pipelines, jobs, tags, groups, compute, store.', examples: ['feed', 'feeds', 'plugins', 'jobs'] },
     { name: 'PACS', blurb: "Ask a PACS for a patient's studies and series, narrow the answer, and pull it into ChRIS.", examples: ['query', 'pull', 'pacs'] },
     { name: 'Admin', blurb: 'Administrative acts that need elevated rights.', examples: ['sudo', 'user'] },
@@ -151,6 +151,64 @@ export const SHELL_TOPICS = [
             '  whatif pl-freesurfer ~/uploads/t1.nii as sub-01',
         ],
     },
+    {
+        name: 'anchors',
+        summary: 'berth anchor <path> [name] and berth close: ChRIS paths downloaded into a berth, and the work returned as one node',
+        page: [
+            'A berth works on its anchors: ChRIS paths downloaded into the berth\'s',
+            'anchors folder, one folder each, through the CUBE API with your token.',
+            'Any path you can read anchors: a node, a folder or file inside its',
+            'output, an upload, a PACS series, /PUBLIC, /SHARED. Several stand at once.',
+            '  berth anchor ~/feeds/feed_5/pl-dircopy_7/pl-fshack_41/data/sub-01',
+            '  berth anchor ~/uploads/weights',
+            '',
+            'The name is the path\'s last part; two paths that end alike need one:',
+            '  berth anchor /PUBLIC/atlas/weights atlas-weights',
+            '',
+            'The node is read from the path alone. Under your own ~/feeds it is the',
+            'plugin instance the path runs through: a path inside a node anchors',
+            'that part only, and a path naming the node anchors its data. Anywhere',
+            'else (uploads, PACS, /PUBLIC, /SHARED, another person\'s home) there is',
+            'none, whatever feed the data sits in.',
+            '',
+            'What refuses, before anything is downloaded:',
+            '  a node that is not finishedSuccessfully, with its status',
+            '  a path in your feeds but at no node (…/feeds/feed_N)',
+            '  a name another path holds, or an anchor that stands (--refresh)',
+            '  a size larger than the anchors folder has free: anchor a folder',
+            '  inside it',
+            '',
+            'The files, the bytes and the free space are said first; above 10 GB',
+            'the anchor asks, and --yes answers. The files are downloaded without',
+            'write permission, which stops an accident, not an intent, and the',
+            'berth keeps a list of them, names and sizes, for its close.',
+            '',
+            'berth close returns the outgoing folder as one node. It writes',
+            'berth.json there (you, every anchor and what it downloaded, the berth,',
+            'the git commit you work in, the image, the time, where the node goes),',
+            'uploads the folder to ~/berth/<uuid>/, and runs pl-dsdircopy over it,',
+            'titled berth work unless --title says otherwise. Where it goes follows',
+            'from the anchors:',
+            '  every anchor under one node   a child of that node',
+            '  no anchor under a node        a new feed: pl-dircopy over every',
+            '                                anchored path, the work its child',
+            '  no anchor at all              a new feed: pl-dircopy over the work',
+            '  two nodes, or node and none   refused: --infeed <anchor> makes it',
+            '                                a child of that anchor\'s node,',
+            '                                --newfeed a new feed over every anchor',
+            '--name names a new feed. When your processes still run in the berth',
+            'the close lists them, with what they hold open in the outgoing folder,',
+            'and asks; --force answers. An anchor with no node whose files changed',
+            'in ChRIS since it was anchored is said and recorded, not refused. A',
+            'node that cannot be made leaves the upload in ~/berth/<uuid>/ and says',
+            'uploaded, not attached. A close removes nothing; a second close is a',
+            'second node.',
+            '',
+            'berth lists the anchors; berth drop <name> removes one, berth clear',
+            'removes all of them and empties the outgoing folder, asking first when',
+            'it holds files not yet closed. ChRIS still holds whatever is removed.',
+        ],
+    },
     { name: 'grep', summary: 'filter text, or a numbered listing keeping its handles' },
     { name: 'command', summary: 'run the system program, not the builtin' },
 ];

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