@fnndsc/brasa 0.46.0 → 0.47.0

package/dist/builtins/res/gather.js

@@ -1,7 +1,7 @@
 /**
  * @file Builtin gather command: the session's cohort as a kernel subject.
  *
- * Subcommands: list (the default), add, remove, clear, name.
+ * Subcommands: list (the default), add, remove, clear, name, feed, process.
  *
  * 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
@@ -17,7 +17,8 @@ import chalk from 'chalk';
 import path from 'path';
 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';
+import { cohort_read, cohort_write, cohortModel_of, cohortFolders_resolve, member_key, members_drop, members_merge, pathKind_determine, seriesUID_ofPath, } from './gather.store.js';
+import { placeImagery_is, seriesFacts_fill } from './gather.facts.js';
 import { envelope_ok, envelope_error } from '@fnndsc/menu';
 import { GATHER_MODEL_KIND } from './gather.kind.js';
 export { GATHER_MODEL_KIND };
@@ -65,7 +66,7 @@ function member_state(member) {
  * @returns A success envelope carrying the rendered table and the model.
  */
 function cohort_render(state) {
-    const model = { kind: GATHER_MODEL_KIND, data: state };
+    const model = cohortModel_of(state);
     if (state.series.length === 0) {
         return envelope_ok(`${chalk.gray('The cohort is empty. Gather something with `gather add <path>`.')}\n`, model);
     }
@@ -121,12 +122,20 @@ async function gather_add(operands) {
                 member.seriesUID = uid;
             member.imagery = true;
         }
+        else if (placeImagery_is(member)) {
+            member.imagery = true;
+        }
         incoming.push(member);
     }
-    const state = await cohort_read();
-    const { members, added, merged } = members_merge(state.series, incoming);
-    state.series = members;
-    await cohort_write(state);
+    await seriesFacts_fill(incoming);
+    const read = await cohort_read();
+    const { members, added, merged } = members_merge(read.series, incoming);
+    read.series = members;
+    await cohort_write(read);
+    // A series CUBE already holds is known by its folder from the moment it
+    // is gathered: that folder is what a surface opens as an image and what
+    // `gather process` roots on. One CUBE read for every series still unplaced.
+    const state = await cohortFolders_resolve(read);
     const noted = [];
     if (added > 0)
         noted.push(`${added} gathered`);
@@ -199,7 +208,27 @@ async function gather_name(operands) {
     }
     state.name = operands.join(' ');
     await cohort_write(state);
-    return envelope_ok(`${chalk.green(`gather: the cohort is "${state.name}".`)}\n`);
+    // The cohort travels with the answer, as every changing verb's does, so
+    // a surface showing it takes the name from here.
+    return envelope_ok(`${chalk.green(`gather: the cohort is "${state.name}".`)}\n`, cohortModel_of(state));
+}
+/**
+ * Makes the cohort's feed, or names the one it has.
+ *
+ * @param words - The words after `gather feed`, raw.
+ * @returns The cohort, with its feed.
+ */
+async function gather_feed(words) {
+    // Loaded on demand, as `process` is: making a feed carries the pull and
+    // feed machinery, which the cohort's own verbs never need.
+    const { cohortFeed_make } = await import('./gather.process.js');
+    const made = await cohortFeed_make(words);
+    if (typeof made === 'string')
+        return gather_error(`gather feed: ${made}`);
+    const feedId = made.state.feed?.feedId;
+    const said = made.made ? `gather: the cohort's feed is ${feedId}, made now.` : `gather: the cohort's feed is ${feedId}.`;
+    const envelope = cohort_render(made.state);
+    return envelope_ok(`${chalk.green(said)}\n${envelope.rendered}`, envelope.model);
 }
 /**
  * Builtin handler for the `gather` command.
@@ -242,10 +271,12 @@ export async function builtin_gather(args) {
         }
         if (subcommand === 'name')
             return await gather_name(operands);
+        if (subcommand === 'feed')
+            return await gather_feed(args.slice(args.indexOf('feed') + 1));
     }
     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|process>`);
+    return gather_error(`Unknown subcommand: ${subcommand}. Usage: gather <list|add|remove|clear|name|feed|process>`);
 }
 //# sourceMappingURL=gather.js.map

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

@@ -1 +1 @@
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package/dist/builtins/res/gather.process.d.ts

@@ -1,4 +1,5 @@
 import { type CommandEnvelope } from '@fnndsc/menu';
+import { type GatherState } from './gather.store.js';
 /** How `gather process` was asked for. */
 export interface GatherProcessArgs {
     /** The plugin or pipeline, as `/bin` names it. */
@@ -19,6 +20,22 @@ export interface GatherProcessArgs {
  * @returns The request, or why it is not one.
  */
 export declare function gatherProcessArgs_parse(words: ReadonlyArray<string>): GatherProcessArgs;
+/**
+ * `gather feed [--title T]`: the cohort's feed, made now when it has none.
+ *
+ * The feed is rooted on every member's place, so a series still at the
+ * PACS is pulled first (one `pull` over all of them); a folder or a file is
+ * already in CUBE and goes into the root as it is. The feed is noted on the
+ * cohort, which is what a later `gather process` runs off and what a
+ * surface reads it from.
+ *
+ * @param words - The words after `gather feed`, raw.
+ * @returns The cohort with its feed, and whether the feed was made now; or a refusal.
+ */
+export declare function cohortFeed_make(words: ReadonlyArray<string>): Promise<{
+    state: GatherState;
+    made: boolean;
+} | string>;
 /**
  * `gather process <name> [--title T] [--detach] [-- args]`: runs a plugin or
  * a pipeline once over the whole cohort.

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

@@ -7,8 +7,8 @@
  * is in the data the plugin reads. This is the shape ARGUS's PROCESS builds
  * from a press (#597), so a manifest and a press make the same feed.
  *
- * When the cohort already has a feed (a `pull --new-feed`, or ARGUS's
- * CREATE FEED, noted it on the cohort), the run goes off that feed's root and
+ * When the cohort already has a feed (`gather feed`, which ARGUS's CREATE
+ * FEED sends, noted it on the cohort), the run goes off that feed's root and
  * nothing is copied twice; otherwise the feed is made here and noted on the
  * cohort for the next run. The name resolves as a bare line resolves it in
  * `/bin`. A series not pulled yet has no folder to copy, and the verb refuses
@@ -28,7 +28,7 @@ import { binExecutableMatches_get } from '../../chris/binExecutables.js';
 import { builtin_executePlugin } from '../pluginExecute.js';
 import { builtin_pipeline } from './pipeline.js';
 import { newFeed_cacheAdd, run_follow } from '../feedCreation.js';
-import { cohort_read, cohort_write } from './gather.store.js';
+import { cohort_read, cohort_write, cohortFolders_resolve } from './gather.store.js';
 /** The usage line a refusal points at. */
 const USAGE = 'gather process <plugin|pipeline> [--title T] [--detach] [-- <its arguments>]';
 /**
@@ -130,6 +130,55 @@ async function cohortFeed_ensure(state, places, title) {
     sink_dataLine(chalk.green(`Feed created: ${feedId} (${places.length} member${places.length === 1 ? '' : 's'} in its root, ${rootInstanceId})`));
     return { feed: made, made: true };
 }
+/**
+ * `gather feed [--title T]`: the cohort's feed, made now when it has none.
+ *
+ * The feed is rooted on every member's place, so a series still at the
+ * PACS is pulled first (one `pull` over all of them); a folder or a file is
+ * already in CUBE and goes into the root as it is. The feed is noted on the
+ * cohort, which is what a later `gather process` runs off and what a
+ * surface reads it from.
+ *
+ * @param words - The words after `gather feed`, raw.
+ * @returns The cohort with its feed, and whether the feed was made now; or a refusal.
+ */
+export async function cohortFeed_make(words) {
+    let title = null;
+    for (let at = 0; at < words.length; at++) {
+        const word = words[at];
+        if (word === '--title') {
+            const given = words[at + 1];
+            if (given === undefined || given.startsWith('--') || given.trim() === '')
+                return '--title needs a title';
+            title = given.trim();
+            at++;
+            continue;
+        }
+        return `${word}: not understood. Usage: gather feed [--title T]`;
+    }
+    let state = await cohortFolders_resolve(await cohort_read());
+    if (state.series.length === 0)
+        return 'the cohort is empty; gather add something first';
+    if (state.feed !== null)
+        return { state, made: false };
+    const away = state.series.filter((member) => member_place(member) === null);
+    if (away.length > 0) {
+        // Loaded on demand: only a cohort with series still at the PACS pulls.
+        const { builtin_pull } = await import('../fs/pull.js');
+        await builtin_pull(away.map((member) => member.vfsPath));
+        state = await cohortFolders_resolve(await cohort_read());
+        const waiting = state.series.filter((member) => member_place(member) === null);
+        if (waiting.length > 0) {
+            const named = waiting.slice(0, 5).map(member_word).join(', ') + (waiting.length > 5 ? `, and ${waiting.length - 5} more` : '');
+            return `${waiting.length} series did not land (${named}); no feed was made`;
+        }
+    }
+    const places = state.series.map((member) => member_place(member));
+    const ensured = await cohortFeed_ensure(state, places, title ?? state.name ?? 'cohort');
+    if (typeof ensured === 'string')
+        return ensured;
+    return { state: { ...state, feed: ensured.feed }, made: ensured.made };
+}
 /**
  * `gather process <name> [--title T] [--detach] [-- args]`: runs a plugin or
  * a pipeline once over the whole cohort.
@@ -142,7 +191,9 @@ export async function gather_process(words) {
     if (parsed.error !== null || parsed.name === null)
         return process_refuse(parsed.error ?? USAGE);
     const name = parsed.name;
-    const state = await cohort_read();
+    // A series pulled but not yet noted on the cohort is found in CUBE, not
+    // refused as never pulled.
+    const state = await cohortFolders_resolve(await cohort_read());
     if (state.series.length === 0)
         return process_refuse('the cohort is empty; gather add something first');
     const waiting = state.series.filter((member) => member_place(member) === null);
@@ -165,7 +216,9 @@ export async function gather_process(words) {
     const { feed, made } = ensured;
     const detach = parsed.detach ? ['--detach'] : [];
     const envelope = matches.pipeline !== undefined
-        ? await builtin_pipeline(['run', name, '--previous', String(feed.rootInstanceId), ...detach, ...parsed.forwarded])
+        // By its /bin name, which names the id: a pipeline found by its CUBE
+        // name runs as exactly that one.
+        ? await builtin_pipeline(['run', matches.pipeline.name, '--previous', String(feed.rootInstanceId), ...detach, ...parsed.forwarded])
         : await builtin_executePlugin(name, [...detach, ...parsed.forwarded], feed.path);
     // The run went off a root, so it reads as continuing a feed; when that
     // feed was made by this line, the answer says so, as a bare run's would.

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

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package/dist/builtins/res/gather.store.d.ts

@@ -1,3 +1,4 @@
+import type { EnvelopeModel } from '@fnndsc/menu';
 /** 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. */
@@ -57,6 +58,16 @@ export interface GatherState {
 }
 /** An empty cohort: what a session that has gathered nothing holds. */
 export declare function cohortState_empty(): GatherState;
+/**
+ * The cohort as the model it travels in.
+ *
+ * Every verb that changes the cohort answers with it, so a surface showing
+ * the cohort redraws from the kernel's copy and never keeps one of its own.
+ *
+ * @param state - The cohort.
+ * @returns The `gather.cohort` model.
+ */
+export declare function cohortModel_of(state: GatherState): EnvelopeModel;
 /**
  * The identity of one member.
  *
@@ -101,10 +112,35 @@ export declare function pathKind_determine(address: string): Promise<GatherKind
 /**
  * The series UID a PACS projection path names, when it names one.
  *
+ * A query's answer names a series `Series_<uid>_<description>`; a path may
+ * also end in the bare UID.
+ *
  * @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;
+/**
+ * Notes on the cohort where the series a pull fetched landed.
+ *
+ * The pull knows each folder the moment CUBE files it; a member that stands
+ * for one of those series takes the folder, so the cohort reads as home
+ * without asking CUBE again.
+ *
+ * @param landed - Series UID to the CUBE folder it landed in.
+ * @returns How many members changed.
+ */
+export declare function cohortFolders_note(landed: ReadonlyMap<string, string>): Promise<number>;
+/**
+ * Asks CUBE where any series member not yet known to be home landed.
+ *
+ * CUBE is the truth and the cohort file a cache of it: a series pulled
+ * earlier, by a surface or in another session, or a folder a surface's
+ * rewrite dropped, is found again here rather than read as never pulled.
+ *
+ * @param state - The cohort, changed in place.
+ * @returns The cohort, with every folder CUBE could name; written back when it changed.
+ */
+export declare function cohortFolders_resolve(state: GatherState): Promise<GatherState>;
 /**
  * Takes members into a cohort, merging what a later sighting knows.
  *

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

@@ -22,11 +22,12 @@
  * @module
  */
 import path from 'path';
-import { listCache_get } from '@fnndsc/cumin';
+import { listCache_get, seriesStorage_resolveMany } 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';
+import { GATHER_MODEL_KIND } from './gather.kind.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. */
@@ -35,6 +36,18 @@ export const COHORT_DIR = '~/gather';
 export function cohortState_empty() {
     return { version: 1, name: null, feed: null, series: [] };
 }
+/**
+ * The cohort as the model it travels in.
+ *
+ * Every verb that changes the cohort answers with it, so a surface showing
+ * the cohort redraws from the kernel's copy and never keeps one of its own.
+ *
+ * @param state - The cohort.
+ * @returns The `gather.cohort` model.
+ */
+export function cohortModel_of(state) {
+    return { kind: GATHER_MODEL_KIND, data: state };
+}
 /**
  * The identity of one member.
  *
@@ -164,12 +177,102 @@ async function folderEntries_list(folder) {
 /**
  * The series UID a PACS projection path names, when it names one.
  *
+ * A query's answer names a series `Series_<uid>_<description>`; a path may
+ * also end in the bare UID.
+ *
  * @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]+)+$/.test(leaf) ? leaf : undefined;
+    if (/^[0-9]+(\.[0-9]+)+$/.test(leaf))
+        return leaf;
+    const named = leaf.match(/^Series_([0-9]+(?:\.[0-9]+)+)(?:_|$)/);
+    return named === null ? undefined : named[1];
+}
+/**
+ * The series UID a member stands for, when it is a series.
+ *
+ * @param member - A cohort member.
+ * @returns The UID it carries, else the one its path names.
+ */
+function memberSeriesUID_get(member) {
+    if (member.kind !== 'series')
+        return undefined;
+    return typeof member.seriesUID === 'string' && member.seriesUID.length > 0
+        ? member.seriesUID
+        : seriesUID_ofPath(member.vfsPath);
+}
+/**
+ * Writes where series landed onto the members that stand for them.
+ *
+ * @param state - The cohort, changed in place.
+ * @param landed - Series UID to the CUBE folder it landed in.
+ * @returns How many members changed.
+ */
+function memberFolders_apply(state, landed) {
+    let changed = 0;
+    for (const member of state.series) {
+        const uid = memberSeriesUID_get(member);
+        if (uid === undefined)
+            continue;
+        const folder = landed.get(uid);
+        if (folder === undefined || member.folderPath === folder)
+            continue;
+        member.seriesUID = uid;
+        member.folderPath = folder;
+        changed += 1;
+    }
+    return changed;
+}
+/**
+ * Notes on the cohort where the series a pull fetched landed.
+ *
+ * The pull knows each folder the moment CUBE files it; a member that stands
+ * for one of those series takes the folder, so the cohort reads as home
+ * without asking CUBE again.
+ *
+ * @param landed - Series UID to the CUBE folder it landed in.
+ * @returns How many members changed.
+ */
+export async function cohortFolders_note(landed) {
+    if (landed.size === 0)
+        return 0;
+    const state = await cohort_read();
+    const changed = memberFolders_apply(state, landed);
+    if (changed > 0)
+        await cohort_write(state);
+    return changed;
+}
+/**
+ * Asks CUBE where any series member not yet known to be home landed.
+ *
+ * CUBE is the truth and the cohort file a cache of it: a series pulled
+ * earlier, by a surface or in another session, or a folder a surface's
+ * rewrite dropped, is found again here rather than read as never pulled.
+ *
+ * @param state - The cohort, changed in place.
+ * @returns The cohort, with every folder CUBE could name; written back when it changed.
+ */
+export async function cohortFolders_resolve(state) {
+    const uids = [...new Set(state.series
+            .filter((member) => typeof member.folderPath !== 'string' || member.folderPath.length === 0)
+            .map(memberSeriesUID_get)
+            .filter((uid) => uid !== undefined))];
+    if (uids.length === 0)
+        return state;
+    const filters = uids.map((uid) => ({ SeriesInstanceUID: uid }));
+    const found = await seriesStorage_resolveMany(filters, { counts: false });
+    if (!found.ok)
+        return state;
+    const landed = new Map();
+    for (const [uid, storage] of found.value) {
+        if (storage.folderPath !== null)
+            landed.set(uid, storage.folderPath);
+    }
+    if (memberFolders_apply(state, landed) > 0)
+        await cohort_write(state);
+    return state;
 }
 /**
  * Takes members into a cohort, merging what a later sighting knows.

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package/dist/builtins/res/play.js

@@ -20,12 +20,13 @@
  * @module
  */
 import chalk from 'chalk';
-import { fileContent_get } from '@fnndsc/salsa';
 import { path_resolve } from '../utils.js';
 import { duration_parse } from '../../lib/duration.js';
 import { recorder_mute, recorder_unmute } from '../../session/recorder.js';
 import { sink_dataLine, sink_errLine } from '../../core/sink.js';
 import { commandCancellation_enable, commandCancellation_signalGet } from '../../core/cancellation.js';
+import { backendInstalled_get } from '../../core/backend.js';
+import { exitCode_read } from '../../core/handlerRun.js';
 import { reference_isReserved, reference_resolve, unresolvedStands_run } from '../../core/expansion.js';
 import { VARIABLE_NAME, variable_get, variableScope_run } from '../../core/variables.js';
 import { shellWords_referencesExpand, shellWords_tokenize } from '../../lib/parser.js';
@@ -110,7 +111,8 @@ async function pause_take(ms, signal) {
     });
 }
 /**
- * Reads a manifest, from the ChRIS filesystem or from the engine's own disk.
+ * Reads a manifest, from the backend's filesystem (ChRIS: CFS) or from the
+ * engine's own disk.
  *
  * A manifest is a ChRIS file: that is what makes one shareable, and sharing
  * it is `setfacl`, like any other file. But a repository's battery lives
@@ -127,11 +129,19 @@ async function manifestText_read(target) {
     // Asking CFS is how we find out whether the manifest lives there. The
     // miss is an ANSWER, not a fault: left on the stack it made a play that
     // ran a host-side battery perfectly exit non-zero.
-    const mark = errorStack.checkpoint_mark();
-    const held = await fileContent_get(resolved);
-    if (held.ok)
-        return { ok: true, value: { text: held.value, from: resolved } };
-    errorStack.checkpoint_drain(mark);
+    // The backend's files are asked first (ChRIS: CFS); a backend with no
+    // files of its own (stratus) has only the engine's disk.
+    const files = backendInstalled_get()?.files;
+    if (files !== undefined) {
+        const mark = errorStack.checkpoint_mark();
+        try {
+            const bytes = await files.read(resolved);
+            return { ok: true, value: { text: bytes.toString('utf8'), from: resolved } };
+        }
+        catch {
+            errorStack.checkpoint_drain(mark);
+        }
+    }
     try {
         const { readFile } = await import('node:fs/promises');
         const text = await readFile(target, 'utf8');
@@ -246,7 +256,7 @@ export async function builtin_play(args) {
     const source = await manifestText_read(parsed.manifest);
     if (!source.ok) {
         process.exitCode = 1;
-        return envelope_error('', undefined, `${chalk.red(`play: cannot read ${parsed.manifest} — no such manifest in the ChRIS filesystem, and none beside the engine.`)}\n`);
+        return envelope_error('', undefined, `${chalk.red(`play: cannot read ${parsed.manifest} — no such manifest in the session's filesystem, and none beside the engine.`)}\n`);
     }
     const manifest = manifest_parse(source.value.text);
     // A manifest may not take a name the session answers for: shadowing a
@@ -294,6 +304,7 @@ export async function builtin_play(args) {
     let stoppedAt = null;
     // What the manifest answers with, read before its scope ends with it.
     let answered;
+    const exitBeforePlay = exitCode_read();
     depth += 1;
     // What a play runs is already written down in the file it is playing: a
     // recording that captured it too would hold every line twice.
@@ -313,10 +324,15 @@ export async function builtin_play(args) {
                 // The line is SHOWN as written, then handed to the session, which
                 // resolves its references the way it resolves every other line's.
                 sink_dataLine(chalk.cyan(`▸ ${line.text}`));
+                // A line failed when it refused or set the exit status. The status is
+                // cleared before each line, so one an earlier command left set (before
+                // the play, or by a line that passed) is never this line's.
+                process.exitCode = 0;
                 const envelopes = await line_execute(line.text);
                 ran += 1;
-                const refused = envelopes.some((envelope) => envelope.status === 'error');
-                if (refused || process.exitCode === 1) {
+                const refused = envelopes.some((envelope) => envelope.status === 'error')
+                    || exitCode_read() !== 0;
+                if (refused) {
                     // A workflow whose first half failed has a second half that is
                     // noise: the play stops where the trouble is.
                     sink_errLine(chalk.red(`✗ ${parsed.manifest}:${line.number} refused — stopping.`));
@@ -337,6 +353,9 @@ export async function builtin_play(args) {
         recorder_unmute();
         depth -= 1;
     }
+    // A play that ran through leaves the session's status as it found it.
+    if (stoppedAt === null)
+        process.exitCode = exitBeforePlay;
     const outcome = {
         manifest: parsed.manifest,
         ran,