@fnndsc/brasa 0.23.2 → 0.25.0

package/dist/builtins/res/gather.js

@@ -0,0 +1,224 @@
+/**
+ * @file Builtin gather command: the session's cohort as a kernel subject.
+ *
+ * Subcommands: list (the default), add, remove, clear, name.
+ *
+ * Gathering was a surface gesture before it was a verb, which meant the set
+ * a session was working on could only be built by pressing on it. As a
+ * subject it is scriptable: a line adds to it, a manifest builds one, and
+ * the surface becomes one client of the cohort rather than the only place
+ * it exists.
+ *
+ * @module
+ */
+import chalk from 'chalk';
+import path from 'path';
+import { envelope_ok, envelope_error } from '@fnndsc/cumin';
+import { table_render } from '@fnndsc/chili/screen/screen.js';
+import { commandArgs_process, path_resolve } from '../utils.js';
+import { cohort_read, cohort_write, member_key, members_drop, members_merge, pathKind_determine, seriesUID_ofPath, } from './gather.store.js';
+/** The model kind under which a cohort travels to a surface. */
+export const GATHER_MODEL_KIND = 'gather.cohort';
+/**
+ * Renders a refusal.
+ *
+ * @param message - What the operator needs to know.
+ * @returns An error envelope, with the process marked failed.
+ */
+function gather_error(message) {
+    process.exitCode = 1;
+    return envelope_error('', undefined, `${chalk.red(message)}\n`);
+}
+/**
+ * What to call a member in a listing.
+ *
+ * @param member - The member to name.
+ * @returns Its description, else the leaf of its path.
+ */
+function member_label(member) {
+    const described = member.description;
+    if (typeof described === 'string' && described.trim().length > 0)
+        return described;
+    return path.posix.basename(member.vfsPath);
+}
+/**
+ * Where a member IS: home in CUBE, or still at the source.
+ *
+ * A series is home once CUBE has said where it landed; a place gathered
+ * from the filesystem was never anywhere else.
+ *
+ * @param member - The member to place.
+ * @returns A one-word state for the listing.
+ */
+function member_state(member) {
+    if (member.kind !== 'series')
+        return 'in CUBE';
+    const landed = member.folderPath;
+    return typeof landed === 'string' && landed.length > 0 ? 'in CUBE' : 'at PACS';
+}
+/**
+ * Renders the cohort as a table, with its name and counts.
+ *
+ * @param state - The cohort to show.
+ * @returns A success envelope carrying the rendered table and the model.
+ */
+function cohort_render(state) {
+    const model = { kind: GATHER_MODEL_KIND, data: state };
+    if (state.series.length === 0) {
+        return envelope_ok(`${chalk.gray('The cohort is empty. Gather something with `gather add <path>`.')}\n`, model);
+    }
+    const rows = state.series.map((member, index) => ({
+        '#': index + 1,
+        kind: member.kind,
+        member: member_label(member),
+        state: member_state(member),
+        path: member.vfsPath,
+    }));
+    const seriesCount = state.series.filter((member) => member.kind === 'series').length;
+    const placeCount = state.series.length - seriesCount;
+    const parts = [];
+    if (seriesCount > 0)
+        parts.push(`${seriesCount} ${seriesCount === 1 ? 'series' : 'series'}`);
+    if (placeCount > 0)
+        parts.push(`${placeCount} ${placeCount === 1 ? 'place' : 'places'}`);
+    const title = state.name === null ? 'Cohort' : `Cohort · ${state.name}`;
+    return envelope_ok(`${table_render(rows, ['#', 'kind', 'member', 'state', 'path'], {
+        title: { title, justification: 'center' },
+    })}${chalk.gray(parts.join(' · '))}\n`, model);
+}
+/**
+ * Takes paths into the cohort.
+ *
+ * Each operand is resolved against the session's cwd, so `gather add .` and
+ * a relative series path mean what they say. What a path IS is asked of the
+ * filesystem rather than guessed from its spelling.
+ *
+ * @param operands - Paths to gather.
+ * @returns The cohort after the change.
+ */
+async function gather_add(operands) {
+    if (operands.length === 0)
+        return gather_error('Usage: gather add <path> [path...]');
+    const incoming = [];
+    for (const operand of operands) {
+        const resolved = await path_resolve(operand);
+        const kind = await pathKind_determine(resolved);
+        // A path that names nothing is refused by name, before anything is
+        // taken: a cohort holding a typo is a cohort a run will be refused on.
+        if (kind === null)
+            return gather_error(`gather: ${resolved}: nothing is there.`);
+        const member = { vfsPath: resolved, kind };
+        if (member.kind === 'series') {
+            const uid = seriesUID_ofPath(resolved);
+            if (uid !== undefined)
+                member.seriesUID = uid;
+            member.imagery = true;
+        }
+        incoming.push(member);
+    }
+    const state = await cohort_read();
+    const { members, added, merged } = members_merge(state.series, incoming);
+    state.series = members;
+    await cohort_write(state);
+    const noted = [];
+    if (added > 0)
+        noted.push(`${added} gathered`);
+    if (merged > 0)
+        noted.push(`${merged} already in the cohort`);
+    const envelope = cohort_render(state);
+    return envelope_ok(`${chalk.green(`gather: ${noted.join(', ')}.`)}\n${envelope.rendered}`, envelope.model);
+}
+/**
+ * Drops members from the cohort, by path or by listing index.
+ *
+ * An index is how the operator reads the cohort back, so `gather remove 2`
+ * removes the second row rather than refusing because 2 is not a path.
+ *
+ * @param operands - Paths or `#`-style indices to drop.
+ * @returns The cohort after the change.
+ */
+async function gather_remove(operands) {
+    if (operands.length === 0)
+        return gather_error('Usage: gather remove <path|index> [path|index...]');
+    const state = await cohort_read();
+    if (state.series.length === 0)
+        return gather_error('gather: the cohort is empty.');
+    const keys = [];
+    for (const operand of operands) {
+        const asIndex = Number.parseInt(operand.replace(/^#/, ''), 10);
+        if (!Number.isNaN(asIndex) && `${asIndex}` === operand.replace(/^#/, '')) {
+            const member = state.series[asIndex - 1];
+            if (member === undefined)
+                return gather_error(`gather: no member ${operand} — the cohort holds ${state.series.length}.`);
+            keys.push(member_key(member));
+            continue;
+        }
+        keys.push(await path_resolve(operand));
+    }
+    const { members, dropped, missing } = members_drop(state.series, keys);
+    if (missing.length > 0) {
+        return gather_error(`gather: not in the cohort: ${missing.join(', ')}`);
+    }
+    state.series = members;
+    await cohort_write(state);
+    const envelope = cohort_render(state);
+    return envelope_ok(`${chalk.green(`gather: ${dropped} removed.`)}\n${envelope.rendered}`, envelope.model);
+}
+/**
+ * Empties the cohort, keeping nothing — not its name, not its feed.
+ *
+ * @returns The empty cohort.
+ */
+async function gather_clear() {
+    const state = await cohort_read();
+    const held = state.series.length;
+    const emptied = { version: state.version, name: null, feed: null, series: [] };
+    await cohort_write(emptied);
+    const envelope = cohort_render(emptied);
+    return envelope_ok(`${chalk.green(`gather: cleared ${held} ${held === 1 ? 'member' : 'members'}.`)}\n${envelope.rendered}`, envelope.model);
+}
+/**
+ * Reads or sets the cohort's name.
+ *
+ * @param operands - The new name, or nothing to read the current one.
+ * @returns The cohort, named.
+ */
+async function gather_name(operands) {
+    const state = await cohort_read();
+    if (operands.length === 0) {
+        if (state.name === null)
+            return envelope_ok(`${chalk.gray('The cohort has no name.')}\n`);
+        return envelope_ok(`${state.name}\n`);
+    }
+    state.name = operands.join(' ');
+    await cohort_write(state);
+    return envelope_ok(`${chalk.green(`gather: the cohort is "${state.name}".`)}\n`);
+}
+/**
+ * Builtin handler for the `gather` command.
+ *
+ * @param args - Parsed command arguments.
+ * @returns An envelope carrying the cohort, or a usage refusal.
+ */
+export async function builtin_gather(args) {
+    const parsed = commandArgs_process(args);
+    const subcommand = parsed._[0];
+    const operands = parsed._.slice(1);
+    try {
+        if (subcommand === undefined || subcommand === 'list')
+            return cohort_render(await cohort_read());
+        if (subcommand === 'add')
+            return await gather_add(operands);
+        if (subcommand === 'remove' || subcommand === 'rm')
+            return await gather_remove(operands);
+        if (subcommand === 'clear')
+            return await gather_clear();
+        if (subcommand === 'name')
+            return await gather_name(operands);
+    }
+    catch (e) {
+        return gather_error(`gather: ${e instanceof Error ? e.message : String(e)}`);
+    }
+    return gather_error(`Unknown subcommand: ${subcommand}. Usage: gather <list|add|remove|clear|name>`);
+}
+//# sourceMappingURL=gather.js.map

package/dist/builtins/res/gather.js.map

@@ -0,0 +1 @@
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package/dist/builtins/res/gather.store.d.ts

@@ -0,0 +1,131 @@
+/** Where the session keeps the cohort it is working on. */
+export declare const COHORT_FILE: string;
+/** The directory that holds it, created on first write. */
+export declare const COHORT_DIR: string;
+/** What a member IS, which decides which verbs can act on it. */
+export type GatherKind = 'series' | 'dir' | 'file';
+/**
+ * One gathered thing.
+ *
+ * `vfsPath` is the identity and the only field the kernel requires; the
+ * rest is what a sighting happened to know. The index signature is not
+ * laxity — it is the promise that a surface's richer record survives a
+ * kernel rewrite untouched.
+ */
+export interface GatherMember {
+    /** The member's address, and its identity within the cohort. */
+    vfsPath: string;
+    /** Series, directory or file. */
+    kind: GatherKind;
+    /** The series UID, when the member is one. */
+    seriesUID?: string;
+    /** What the member is called where it came from. */
+    description?: string;
+    /** The modality, for a series. */
+    modality?: string;
+    /** The patient it came from, for a series. */
+    patient?: string;
+    /** The study it came from, for a series. */
+    study?: string;
+    /** Whether the member is imagery: a series always is, a place sometimes. */
+    imagery?: boolean;
+    /** Its ChRIS folder once CUBE has said where it landed. */
+    folderPath?: string;
+    /** How many files it holds, when the source said. */
+    files?: number;
+    /** Anything a surface knows and the kernel does not, kept across a write. */
+    [extra: string]: unknown;
+}
+/** The feed a cohort was rooted in: its id, and the root a run appends to. */
+export interface GatherFeed {
+    feedId: number;
+    rootInstanceId: number;
+    path: string;
+}
+/**
+ * The whole cohort as it is kept on disk.
+ *
+ * The member array is named `series` because that is what the surface
+ * wrote before members had kinds, and a rename would strand every cohort
+ * a session is currently holding for no gain.
+ */
+export interface GatherState {
+    version: number;
+    name: string | null;
+    feed: GatherFeed | null;
+    series: GatherMember[];
+}
+/** An empty cohort: what a session that has gathered nothing holds. */
+export declare function cohortState_empty(): GatherState;
+/**
+ * The identity of one member.
+ *
+ * Path first, falling back to the series UID for a record written before
+ * membership was path-keyed, so an older cohort still de-duplicates.
+ *
+ * @param member - The member to key.
+ * @returns Its identity within the cohort.
+ */
+export declare function member_key(member: GatherMember): string;
+/**
+ * Reads the cohort the session is working on.
+ *
+ * An unreadable or unparseable file answers an EMPTY cohort rather than an
+ * error: this is a working file the operator may have edited, and a cohort
+ * that cannot be read is not a reason to refuse the command.
+ *
+ * @returns The cohort, normalized.
+ */
+export declare function cohort_read(): Promise<GatherState>;
+/**
+ * Writes the cohort back, and tells the listing cache the folder changed.
+ *
+ * Without the invalidation an `ls ~/gather` right after a gather serves the
+ * listing from before the write and the operator is told their cohort does
+ * not exist — the same staleness a CSV export once showed.
+ *
+ * @param state - The cohort to keep.
+ */
+export declare function cohort_write(state: GatherState): Promise<void>;
+/**
+ * Says what a path IS, by asking rather than by guessing at its spelling.
+ *
+ * A PACS projection is a series: the query answer's own addresses are the
+ * only things in the tree that name one. Everything else is asked of the
+ * filesystem, and what is not a directory is a file.
+ *
+ * @param address - A resolved VFS path.
+ * @returns The member kind to record, or null when nothing is at the path.
+ */
+export declare function pathKind_determine(address: string): Promise<GatherKind | null>;
+/**
+ * The series UID a PACS projection path names, when it names one.
+ *
+ * @param address - A resolved VFS path.
+ * @returns The UID, or undefined when the path is not a series projection.
+ */
+export declare function seriesUID_ofPath(address: string): string | undefined;
+/**
+ * Takes members into a cohort, merging what a later sighting knows.
+ *
+ * @param held - The members already in the cohort, in gather order.
+ * @param incoming - The members being taken.
+ * @returns The new membership, and how many were new rather than merged.
+ */
+export declare function members_merge(held: GatherMember[], incoming: GatherMember[]): {
+    members: GatherMember[];
+    added: number;
+    merged: number;
+};
+/**
+ * Drops members by identity.
+ *
+ * @param held - The current membership.
+ * @param keys - Identities to drop.
+ * @returns The remaining members, and the identities that matched nothing.
+ */
+export declare function members_drop(held: GatherMember[], keys: string[]): {
+    members: GatherMember[];
+    dropped: number;
+    missing: string[];
+};

package/dist/builtins/res/gather.store.js

@@ -0,0 +1,225 @@
+/**
+ * @file The session's cohort, as the kernel holds it.
+ *
+ * A cohort is the set of things a session is working on — a PACS series
+ * still at the modality, a directory of uploads, one file — gathered so
+ * that one act can be taken over all of them. It belongs to the SESSION,
+ * not to a surface: it outlives a page refresh, a second surface attached
+ * to the same session sees the same one, and a command line reaches it
+ * without a browser in the room.
+ *
+ * Membership is keyed by PATH. A series, a directory and a file are all
+ * addressable, so one identity rule covers every kind, gathering the same
+ * thing twice merges rather than doubles, and `gather remove` takes the
+ * same operand whatever it is removing.
+ *
+ * The cohort lives as a working file in the ChRIS filesystem, in the shape
+ * the surface already wrote, so the two read each other's cohorts without
+ * a migration. Fields this layer does not understand are preserved across
+ * a rewrite: the surface knows things about a series that the kernel has
+ * no name for, and a kernel write must not quietly forget them.
+ *
+ * @module
+ */
+import path from 'path';
+import { listCache_get } from '@fnndsc/cumin';
+import { fileContent_get, files_path_isDirectory } from '@fnndsc/salsa';
+import { files_touch as chefs_touch_cmd } from '@fnndsc/chili/commands/fs/touch.js';
+import { files_mkdir as chefs_mkdir_cmd } from '@fnndsc/chili/commands/fs/mkdir.js';
+import { path_resolve } from '../utils.js';
+/** Where the session keeps the cohort it is working on. */
+export const COHORT_FILE = '~/gather/current.json';
+/** The directory that holds it, created on first write. */
+export const COHORT_DIR = '~/gather';
+/** An empty cohort: what a session that has gathered nothing holds. */
+export function cohortState_empty() {
+    return { version: 1, name: null, feed: null, series: [] };
+}
+/**
+ * The identity of one member.
+ *
+ * Path first, falling back to the series UID for a record written before
+ * membership was path-keyed, so an older cohort still de-duplicates.
+ *
+ * @param member - The member to key.
+ * @returns Its identity within the cohort.
+ */
+export function member_key(member) {
+    const address = member.vfsPath;
+    if (typeof address === 'string' && address.length > 0)
+        return address;
+    const uid = member.seriesUID;
+    return typeof uid === 'string' ? uid : '';
+}
+/**
+ * Fills in what an older or partial record left out.
+ *
+ * A record written before kinds existed is a series, which is what every
+ * member was then; a record written before paths were identity carries its
+ * address in `seriesUID`.
+ *
+ * @param raw - One entry as the file held it.
+ * @returns The same entry, normalized.
+ */
+function member_normalize(raw) {
+    const normalized = { ...raw };
+    if (typeof normalized.vfsPath !== 'string' || normalized.vfsPath.length === 0) {
+        normalized.vfsPath = typeof raw.seriesUID === 'string' ? raw.seriesUID : '';
+    }
+    if (normalized.kind !== 'dir' && normalized.kind !== 'file' && normalized.kind !== 'series') {
+        normalized.kind = 'series';
+    }
+    return normalized;
+}
+/**
+ * Reads the cohort the session is working on.
+ *
+ * An unreadable or unparseable file answers an EMPTY cohort rather than an
+ * error: this is a working file the operator may have edited, and a cohort
+ * that cannot be read is not a reason to refuse the command.
+ *
+ * @returns The cohort, normalized.
+ */
+export async function cohort_read() {
+    try {
+        const resolved = await path_resolve(COHORT_FILE);
+        const content = await fileContent_get(resolved);
+        if (!content.ok)
+            return cohortState_empty();
+        const held = JSON.parse(content.value);
+        const members = Array.isArray(held.series)
+            ? held.series.map(member_normalize).filter((m) => m.vfsPath.length > 0)
+            : [];
+        return {
+            version: typeof held.version === 'number' ? held.version : 1,
+            name: typeof held.name === 'string' ? held.name : null,
+            feed: (held.feed ?? null),
+            series: members,
+        };
+    }
+    catch {
+        return cohortState_empty();
+    }
+}
+/**
+ * Writes the cohort back, and tells the listing cache the folder changed.
+ *
+ * Without the invalidation an `ls ~/gather` right after a gather serves the
+ * listing from before the write and the operator is told their cohort does
+ * not exist — the same staleness a CSV export once showed.
+ *
+ * @param state - The cohort to keep.
+ */
+export async function cohort_write(state) {
+    const directory = await path_resolve(COHORT_DIR);
+    await chefs_mkdir_cmd(directory);
+    const target = await path_resolve(COHORT_FILE);
+    await chefs_touch_cmd(target, { withContents: JSON.stringify(state) });
+    const cache = listCache_get();
+    cache.cache_invalidate(path.posix.dirname(target));
+}
+/**
+ * Says what a path IS, by asking rather than by guessing at its spelling.
+ *
+ * A PACS projection is a series: the query answer's own addresses are the
+ * only things in the tree that name one. Everything else is asked of the
+ * filesystem, and what is not a directory is a file.
+ *
+ * @param address - A resolved VFS path.
+ * @returns The member kind to record, or null when nothing is at the path.
+ */
+export async function pathKind_determine(address) {
+    if (address.startsWith('/net/pacs/'))
+        return 'series';
+    try {
+        if (await files_path_isDirectory(address))
+            return 'dir';
+        // Not a directory is not the same as a file: a path that names nothing
+        // must not be gathered as one, or a typo becomes a member a run would
+        // be handed and refused on. Its parent is asked whether it is there.
+        const parent = path.posix.dirname(address);
+        const leaf = path.posix.basename(address);
+        const listed = await folderEntries_list(parent);
+        if (!listed.ok || !listed.value.includes(leaf))
+            return null;
+        return 'file';
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * The names a folder holds, files and folders alike.
+ *
+ * @param folder - The folder to list.
+ * @returns Its entries' names, or a refusal when it cannot be listed.
+ */
+async function folderEntries_list(folder) {
+    const { vfsDispatcher } = await import('@fnndsc/salsa');
+    const listed = await vfsDispatcher.list(folder);
+    if (!listed.ok)
+        return { ok: false };
+    return { ok: true, value: listed.value.map((item) => item.name) };
+}
+/**
+ * The series UID a PACS projection path names, when it names one.
+ *
+ * @param address - A resolved VFS path.
+ * @returns The UID, or undefined when the path is not a series projection.
+ */
+export function seriesUID_ofPath(address) {
+    const leaf = path.posix.basename(address);
+    return /^[0-9]+(\.[0-9]+)+$/.test(leaf) ? leaf : undefined;
+}
+/**
+ * Takes members into a cohort, merging what a later sighting knows.
+ *
+ * @param held - The members already in the cohort, in gather order.
+ * @param incoming - The members being taken.
+ * @returns The new membership, and how many were new rather than merged.
+ */
+export function members_merge(held, incoming) {
+    const byKey = new Map(held.map((member) => [member_key(member), member]));
+    let added = 0;
+    let merged = 0;
+    for (const member of incoming) {
+        const key = member_key(member);
+        if (key.length === 0)
+            continue;
+        const existing = byKey.get(key);
+        if (existing === undefined) {
+            byKey.set(key, member);
+            added += 1;
+            continue;
+        }
+        byKey.set(key, { ...existing, ...member });
+        merged += 1;
+    }
+    return { members: [...byKey.values()], added, merged };
+}
+/**
+ * Drops members by identity.
+ *
+ * @param held - The current membership.
+ * @param keys - Identities to drop.
+ * @returns The remaining members, and the identities that matched nothing.
+ */
+export function members_drop(held, keys) {
+    const wanted = new Set(keys);
+    const kept = [];
+    const hit = new Set();
+    for (const member of held) {
+        const key = member_key(member);
+        if (wanted.has(key)) {
+            hit.add(key);
+            continue;
+        }
+        kept.push(member);
+    }
+    return {
+        members: kept,
+        dropped: held.length - kept.length,
+        missing: keys.filter((key) => !hit.has(key)),
+    };
+}
+//# sourceMappingURL=gather.store.js.map

package/dist/builtins/res/gather.store.js.map

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package/dist/builtins/res/pipeline.args.d.ts

@@ -14,11 +14,14 @@ export interface PipelineRunOverrides {
     previousOverride: number | undefined;
     paramFile: string | undefined;
     bindings: PipelineInvocationBinding[];
+    /** Whether the operator asked for the handle rather than the outcome. */
+    detach: boolean;
     parseError: string | null;
 }
 /**
- * Parses `--compute <resource>` and `--previous <inst_id>` overrides from
- * `pipeline run <name|id> ...` arguments (scanning from index 2).
+ * Parses `--compute <resource>`, `--previous <inst_id>`, `--paramFile <path>`
+ * and `--detach` from `pipeline run <name|id> ...` arguments (scanning from
+ * index 2). Anything else in `--node.field value` form is a binding.
  *
  * @param args - The full `pipeline run` argument list.
  * @returns The parsed overrides.

package/dist/builtins/res/pipeline.args.js

@@ -1,7 +1,8 @@
 import { executableArguments_parse } from '../argumentTokens.js';
 /**
- * Parses `--compute <resource>` and `--previous <inst_id>` overrides from
- * `pipeline run <name|id> ...` arguments (scanning from index 2).
+ * Parses `--compute <resource>`, `--previous <inst_id>`, `--paramFile <path>`
+ * and `--detach` from `pipeline run <name|id> ...` arguments (scanning from
+ * index 2). Anything else in `--node.field value` form is a binding.
  *
  * @param args - The full `pipeline run` argument list.
  * @returns The parsed overrides.
@@ -11,6 +12,7 @@ export function pipelineRunArgs_parse(args) {
     let previousOverride;
     let paramFile;
     const bindings = [];
+    let detach = false;
     let parseError = null;
     for (let i = 2; i < args.length; i++) {
         const token = args[i];
@@ -32,6 +34,9 @@ export function pipelineRunArgs_parse(args) {
             previousOverride = Number(value);
             i++;
         }
+        else if (token === '--detach') {
+            detach = true;
+        }
         else if (token === '--paramFile') {
             const value = args[i + 1];
             if (paramFile !== undefined) {
@@ -74,6 +79,6 @@ export function pipelineRunArgs_parse(args) {
             break;
         }
     }
-    return { computeOverride, previousOverride, paramFile, bindings, parseError };
+    return { computeOverride, previousOverride, paramFile, bindings, detach, parseError };
 }
 //# sourceMappingURL=pipeline.args.js.map