@fnndsc/brasa 0.46.0 → 0.48.0

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_wrap(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;
+export declare function seriesUID_parse(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_wrap(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) {
+export function seriesUID_parse(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_parse(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/group.js

@@ -6,7 +6,7 @@
  * Singular/plural aliases: group / groups
  */
 import chalk from 'chalk';
-import { commandArgs_process, cliOptions_from } from '../utils.js';
+import { commandArgs_process, cliOptions_extract, resourceListOptions_refusal, resourceSearchTerm_refusal, resourceSearch_args } from '../utils.js';
 import { groups_fetchList } from '@fnndsc/chili/commands/groups/list.js';
 import { groupFields_fetch } from '@fnndsc/chili/commands/groups/fields.js';
 import { groupMembers_fetch, groupReference_resolve, groupUser_add, groupUser_remove, } from '@fnndsc/chili/commands/groups/membership.js';
@@ -117,8 +117,13 @@ export async function builtin_group(args) {
     const parsed = commandArgs_process(args);
     const subcommand = parsed._[0];
     if (!subcommand || subcommand === 'list') {
+        const refusal = resourceListOptions_refusal('group', parsed);
+        if (refusal !== null) {
+            process.exitCode = 1;
+            return envelope_error('', undefined, `${chalk.red(refusal)}\n`);
+        }
         try {
-            const { groups, selectedFields, totalCount } = await groups_fetchList(cliOptions_from(parsed));
+            const { groups, selectedFields, totalCount } = await groups_fetchList(cliOptions_extract(parsed));
             if (groups.length === 0) {
                 return envelope_ok(`${chalk.gray('No groups found.')}\n`);
             }
@@ -130,9 +135,14 @@ export async function builtin_group(args) {
         }
     }
     if (subcommand === 'search') {
-        const query = parsed._[1] ?? '';
+        const refusal = resourceSearchTerm_refusal('group', parsed);
+        if (refusal !== null) {
+            process.exitCode = 1;
+            return envelope_error('', undefined, `${chalk.red(refusal)}\n`);
+        }
+        const query = String(parsed._[1]);
         const search = query.includes(':') ? query : `name_icontains:${query}`;
-        return builtin_group(['--search', search]);
+        return builtin_group(resourceSearch_args(parsed, search));
     }
     if (subcommand === 'inspect') {
         const reference = parsed._[1];

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

@@ -1 +1 @@
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package/dist/builtins/res/pipeline.js

@@ -24,7 +24,7 @@ import { table_render } from '@fnndsc/chili/screen/screen.js';
 import { args_checkHasHelpFlag, help_render } from '../help.js';
 import { sink_get, sink_dataLine, sink_errLine } from '../../core/sink.js';
 import { pipelineRunArgs_parse } from './pipeline.args.js';
-import { runs_awaitSettled, settlement_render, settlementStatus_of } from './runWait.js';
+import { runs_awaitSettled, settlement_render, settlementStatus_derive } from './runWait.js';
 import { pipelineDiagram_handle } from './pipeline.diagram.js';
 import { pipelineManifest_render, pipelineParameters_render } from './pipeline.manifest.js';
 import { path_resolve } from '../utils.js';
@@ -252,7 +252,7 @@ export function pipelineScheduled_make(pipelineName, workflowId, feedId, instanc
             instanceId,
             pluginName: known?.pluginName ?? 'unknown',
             outputPath: known?.outputPath ?? null,
-            status: settlement === null ? 'detached' : settlementStatus_of(settlement, instanceId),
+            status: settlement === null ? 'detached' : settlementStatus_derive(settlement, instanceId),
         };
     });
     const parents = new Set(instanceIds

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

@@ -1 +1 @@
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package/dist/builtins/res/play.js

@@ -20,14 +20,17 @@
  * @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 { reference_isReserved, reference_resolve, unresolvedStands_run } from '../../core/expansion.js';
-import { VARIABLE_NAME, variable_get, variableScope_run } from '../../core/variables.js';
+import { backendInstalled_get } from '../../core/backend.js';
+import { exitCode_read } from '../../core/handlerRun.js';
+import { reference_changedBy, reference_isReserved, reference_resolve, unresolvedStands_run } from '../../core/expansion.js';
+import { pipes_parse } from '../../core/preprocess.js';
+import { semicolons_parse } from '../../lib/semicolonParser.js';
+import { VARIABLE_NAME, assignment_parse, variable_get, variableScope_run } from '../../core/variables.js';
 import { shellWords_referencesExpand, shellWords_tokenize } from '../../lib/parser.js';
 import { errorStack } from '@fnndsc/fond';
 import { envelope_ok, envelope_error } from '@fnndsc/menu';
@@ -110,7 +113,8 @@ 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 +131,19 @@ 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');
@@ -142,23 +154,74 @@ async function manifestText_read(target) {
     }
 }
 /**
- * Renders a line as the kernel would expand it, without running it.
+ * Renders one command's words as the kernel would expand them.
  *
  * It expands through the SAME resolver the dispatcher uses, so a dry run
- * cannot disagree with a play; it simply stops before acting.
+ * cannot disagree with a play; it simply stops before acting. A reference
+ * an earlier line may have changed stands as written: the session could
+ * answer it, but from the state before the play, which the manifest has
+ * since changed.
  *
- * @param text - The line as the manifest holds it.
- * @returns The line with its references filled in.
+ * @param text - The command as the manifest holds it.
+ * @param passed - What the lines before it could have changed.
+ * @returns The command with its references filled in.
  */
-async function line_preview(text) {
+async function words_preview(text, passed) {
     const words = shellWords_tokenize(text);
-    const expanded = await unresolvedStands_run(async () => await shellWords_referencesExpand(words, reference_resolve, true));
+    const resolve = async (name) => (reference_changedBy(name, passed) ? null : await reference_resolve(name));
+    const expanded = await unresolvedStands_run(async () => await shellWords_referencesExpand(words, resolve, true));
     if (!expanded.ok)
         return text;
     return expanded.words
         .map((word) => (/\s/.test(word.value) ? `'${word.value}'` : word.value))
         .join(' ');
 }
+/**
+ * Renders a line as the kernel would expand it, without running it.
+ *
+ * The line is taken apart as the session takes it: a batch at its `;`, and
+ * a capture `NAME=$(…)` around the command it holds, which plain words
+ * would split through, closing parenthesis and all.
+ *
+ * @param text - The line as the manifest holds it.
+ * @param passed - What the lines before it could have changed.
+ * @returns The line with its references filled in.
+ */
+async function line_preview(text, passed) {
+    const parts = [];
+    for (const command of semicolons_parse(text.trim())) {
+        const assignment = assignment_parse(command.trim());
+        parts.push(assignment !== null && 'capture' in assignment
+            ? `${assignment.name}=$(${await words_preview(assignment.capture, passed)})`
+            : await words_preview(command, passed));
+    }
+    return parts.join('; ');
+}
+/**
+ * Notes what a line could change, for the lines a dry run previews after
+ * it: the verb of every command it holds (each side of a pipe, each part of
+ * a batch, the command a capture runs) and the variable it assigns.
+ *
+ * @param text - The line as the manifest holds it.
+ * @param verbs - The verbs seen so far, added to.
+ * @param assigned - The variables assigned so far, added to.
+ */
+function linePassed_note(text, verbs, assigned) {
+    for (const command of semicolons_parse(text.trim())) {
+        const assignment = assignment_parse(command.trim());
+        if (assignment !== null)
+            assigned.add(assignment.name);
+        if (assignment !== null && !('capture' in assignment))
+            continue;
+        const body = assignment !== null && 'capture' in assignment ? assignment.capture : command;
+        for (const piece of pipes_parse(body)) {
+            const words = shellWords_tokenize(piece).map((word) => word.value);
+            const verb = words[0] === 'sudo' ? words[1] : words[0];
+            if (verb !== undefined)
+                verbs.add(verb);
+        }
+    }
+}
 /**
  * Parses `play`'s own arguments.
  *
@@ -246,7 +309,7 @@ export async function builtin_play(args) {
     const source = await manifestText_read(parsed.manifest);
     if (!source.ok) {
         process.exitCode = 1;
-        return envelope_error('', undefined, `${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 +357,10 @@ export async function builtin_play(args) {
     let stoppedAt = null;
     // What the manifest answers with, read before its scope ends with it.
     let answered;
+    // What the lines a dry run passed over could have changed.
+    const passedVerbs = new Set();
+    const passedAssigned = new Set();
+    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.
@@ -304,19 +371,25 @@ export async function builtin_play(args) {
                 // A dry run shows what WOULD run, expanded by the kernel's own
                 // expander rather than a second one living here: a reference nothing
                 // can answer yet stands as written, since nothing has run to give it
-                // a value.
+                // a value, and so does one an earlier line may have changed (#1241).
                 if (parsed.dryRun) {
-                    sink_dataLine(chalk.cyan(`▸ ${await line_preview(line.text)}`));
+                    sink_dataLine(chalk.cyan(`▸ ${await line_preview(line.text, { count: ran, verbs: passedVerbs, assigned: passedAssigned })}`));
+                    linePassed_note(line.text, passedVerbs, passedAssigned);
                     ran += 1;
                     continue;
                 }
                 // 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 +410,9 @@ 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,