@fnndsc/brasa 0.46.0 → 0.48.0

package/dist/builtins/res/feed.tree.render.js

@@ -95,7 +95,7 @@ function feedFlatNodes_build(graph, roots) {
     });
 }
 /** Converts one collapsed feed node into the shared diagram model. */
-function collapsedNode_toDiagram(node) {
+function collapsedNode_convertToDiagram(node) {
     const functionName = node.count === 1
         ? `${node.pluginName}_${node.memberIds[0]}`
         : `${node.pluginName}_x${node.count}_${node.memberIds[0]}`;
@@ -109,7 +109,7 @@ function collapsedNode_toDiagram(node) {
         hasJoin: node.hasJoin,
         joinParentIDs: node.joinParentIDs,
         arguments: [],
-        children: node.children.map((child) => collapsedNode_toDiagram(child)),
+        children: node.children.map((child) => collapsedNode_convertToDiagram(child)),
     };
 }
 /**
@@ -123,7 +123,7 @@ function collapsedNode_toDiagram(node) {
 export function feedDiagramNodes_build(graph, roots, flat = false) {
     return flat
         ? feedFlatNodes_build(graph, roots)
-        : collapse_build(graph, roots).map((node) => collapsedNode_toDiagram(node));
+        : collapse_build(graph, roots).map((node) => collapsedNode_convertToDiagram(node));
 }
 /**
  * Pure render of a {@link FeedGraph} into an annotated tree. Collapses isomorphic siblings

package/dist/builtins/res/feed.tree.render.js.map

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

@@ -3,7 +3,7 @@
  * Manages file resources.
  */
 import chalk from 'chalk';
-import { commandArgs_process, cliOptions_from } from '../utils.js';
+import { commandArgs_process, cliOptions_extract } from '../utils.js';
 import { files_fetchList } from '@fnndsc/chili/commands/files/list.js';
 import { fileFields_fetch } from '@fnndsc/chili/commands/files/fields.js';
 import { table_render } from '@fnndsc/chili/screen/screen.js';
@@ -24,7 +24,7 @@ async function builtin_fileGroup(args, assetName) {
     try {
         if (subcommand === 'list') {
             const path = parsed._[1];
-            const results = await files_fetchList(cliOptions_from(parsed), assetName, path);
+            const results = await files_fetchList(cliOptions_extract(parsed), assetName, path);
             if (!results) {
                 return envelope_error('', undefined, `No ${assetName} resources found. Perhaps check your current context?\n`);
             }

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

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

@@ -0,0 +1,18 @@
+import type { GatherMember } from './gather.store.js';
+/**
+ * Fills in each series member's facts from the query answer its path names.
+ *
+ * A fact the answer does not have is left as it was, and an answer that
+ * cannot be read leaves the member bare: these are what a listing shows,
+ * and none of them is a reason to refuse the gather.
+ *
+ * @param members - Members being gathered, changed in place.
+ */
+export declare function seriesFacts_fill(members: GatherMember[]): Promise<void>;
+/**
+ * Whether a gathered folder is imagery, by its name and place.
+ *
+ * @param member - A member being gathered.
+ * @returns True for a directory that holds one series.
+ */
+export declare function placeImagery_is(member: GatherMember): boolean;

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

@@ -0,0 +1,114 @@
+/**
+ * @file What a gathered member is, told by the kernel rather than a surface.
+ *
+ * A member is stored by its path; what a listing shows about it — a series'
+ * description, modality, patient and study, whether a folder is imagery —
+ * is filled in here when it is gathered, so every surface reads the same
+ * row and none of them has to carry facts into the cohort itself.
+ *
+ * A series' facts come from the query answer its path names. The PACS
+ * mount already holds that answer decoded (the operator listed it to find
+ * the series), so this is usually a cache read and at most one CUBE read
+ * per query. A folder's imagery comes from its name and place alone.
+ *
+ * @module
+ */
+import path from 'path';
+import { queryId_extractFromFolder } from '@fnndsc/salsa';
+import { seriesFolder_is } from '@fnndsc/menu';
+/**
+ * The query a PACS path lives under: its id and its folder's path.
+ *
+ * @param address - A resolved `/net/pacs/queries/...` path.
+ * @returns The query, or null when the path names none.
+ */
+function pathQuery_parse(address) {
+    if (!address.startsWith('/net/pacs/'))
+        return null;
+    const parts = address.split('/').filter(Boolean);
+    const at = parts.findIndex((part) => /_qid:\d+/.test(part));
+    if (at === -1)
+        return null;
+    const queryId = queryId_extractFromFolder(parts[at]);
+    if (Number.isNaN(queryId))
+        return null;
+    return { queryId, folder: `/${parts.slice(0, at + 1).join('/')}` };
+}
+/**
+ * Every series one query answered, by series UID.
+ *
+ * @param queryId - The query.
+ * @param folder - Its folder, which the answer's paths are built under.
+ * @returns The series, or an empty map when the answer cannot be read.
+ */
+async function answerSeries_get(queryId, folder) {
+    const byUID = new Map();
+    const { vfsDispatcher } = await import('@fnndsc/salsa');
+    const decoded = await vfsDispatcher.pacs.queryResult_fetch(queryId);
+    if (decoded === null || decoded.json === undefined || decoded.json === null)
+        return byUID;
+    // Loaded on demand: only a series gathered from an answer needs it.
+    const { pacsQueryModel_build } = await import('../net/query.model.js');
+    const model = pacsQueryModel_build(decoded, { queryId, vfsPath: folder, pacsName: '', expression: '' });
+    for (const study of model.studies) {
+        for (const series of study.series)
+            byUID.set(series.seriesUID, { series, study });
+    }
+    return byUID;
+}
+/**
+ * Fills in each series member's facts from the query answer its path names.
+ *
+ * A fact the answer does not have is left as it was, and an answer that
+ * cannot be read leaves the member bare: these are what a listing shows,
+ * and none of them is a reason to refuse the gather.
+ *
+ * @param members - Members being gathered, changed in place.
+ */
+export async function seriesFacts_fill(members) {
+    const queries = new Map();
+    for (const member of members) {
+        if (member.kind !== 'series' || member.seriesUID === undefined)
+            continue;
+        const query = pathQuery_parse(member.vfsPath);
+        if (query !== null)
+            queries.set(query.queryId, query.folder);
+    }
+    const answered = new Map();
+    for (const [queryId, folder] of queries)
+        answered.set(queryId, await answerSeries_get(queryId, folder));
+    for (const member of members) {
+        if (member.kind !== 'series' || member.seriesUID === undefined)
+            continue;
+        const query = pathQuery_parse(member.vfsPath);
+        if (query === null)
+            continue;
+        const found = answered.get(query.queryId)?.get(member.seriesUID);
+        if (found === undefined)
+            continue;
+        const { series, study } = found;
+        if (series.description !== '')
+            member.description = series.description;
+        if (series.modality !== '')
+            member.modality = series.modality;
+        if (series.fileCount !== undefined)
+            member.files = series.fileCount;
+        // MRN first, as the PACS listing reads a patient; the name when the
+        // answer carries no identifier.
+        const patient = study.patientId || study.patientName;
+        if (patient !== '')
+            member.patient = patient;
+        if (study.description !== '')
+            member.study = study.description;
+    }
+}
+/**
+ * Whether a gathered folder is imagery, by its name and place.
+ *
+ * @param member - A member being gathered.
+ * @returns True for a directory that holds one series.
+ */
+export function placeImagery_is(member) {
+    return member.kind === 'dir' && seriesFolder_is(member.vfsPath, path.posix.basename(member.vfsPath));
+}
+//# sourceMappingURL=gather.facts.js.map

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

@@ -0,0 +1 @@
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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
@@ -11,13 +11,14 @@
  *
  * @module
  */
-import { listingIn_take, listingOperands_of } from '../../core/listing.js';
-import { answerNumbering_of, handleWords_of, numberedFooter_of } from '../../session/answer.js';
+import { listingIn_take, listingOperands_extract } from '../../core/listing.js';
+import { answerNumbering_derive, handleWords_map, numberedFooter_render } from '../../session/answer.js';
 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_wrap, cohortFolders_resolve, member_key, members_drop, members_merge, pathKind_determine, seriesUID_parse, } 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 };
@@ -65,14 +66,14 @@ 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_wrap(state);
     if (state.series.length === 0) {
         return envelope_ok(`${chalk.gray('The cohort is empty. Gather something with `gather add <path>`.')}\n`, model);
     }
     // Each member wears the handle an index expands to (#1099): one sequence
     // per kind, as the cohort's numbering counts them.
-    const numbered = answerNumbering_of(GATHER_MODEL_KIND, state) ?? [];
-    const words = handleWords_of(numbered);
+    const numbered = answerNumbering_derive(GATHER_MODEL_KIND, state) ?? [];
+    const words = handleWords_map(numbered);
     const kindCode = (member) => (member.kind === 'dir' ? 'DIR' : member.kind === 'file' ? 'FIL' : 'SER');
     const rows = state.series.map((member) => ({
         '@': words.get(`${kindCode(member)}:${member.vfsPath}`) ?? '',
@@ -91,7 +92,7 @@ function cohort_render(state) {
     const title = state.name === null ? 'Cohort' : `Cohort · ${state.name}`;
     return envelope_ok(`${table_render(rows, ['@', 'kind', 'member', 'state', 'path'], {
         title: { title, justification: 'center' },
-    })}${chalk.gray(parts.join(' · '))}\n${numbered.length > 0 ? `${chalk.gray(numberedFooter_of(numbered))}\n` : ''}`, model);
+    })}${chalk.gray(parts.join(' · '))}\n${numbered.length > 0 ? `${chalk.gray(numberedFooter_render(numbered))}\n` : ''}`, model);
 }
 /**
  * Takes paths into the cohort.
@@ -116,17 +117,25 @@ async function gather_add(operands) {
             return gather_error(`gather: ${resolved}: nothing is there.`);
         const member = { vfsPath: resolved, kind };
         if (member.kind === 'series') {
-            const uid = seriesUID_ofPath(resolved);
+            const uid = seriesUID_parse(resolved);
             if (uid !== undefined)
                 member.seriesUID = uid;
             member.imagery = true;
         }
+        else if (placeImagery_is(member)) {
+            member.imagery = true;
+        }
         incoming.push(member);
     }
-    const state = await cohort_read();
-    const { members, added, merged } = members_merge(state.series, incoming);
-    state.series = members;
-    await cohort_write(state);
+    await seriesFacts_fill(incoming);
+    const read = await cohort_read();
+    const { members, added, merged } = members_merge(read.series, incoming);
+    read.series = members;
+    await cohort_write(read);
+    // A series CUBE already holds is known by its folder from the moment it
+    // is gathered: that folder is what a surface opens as an image and what
+    // `gather process` roots on. One CUBE read for every series still unplaced.
+    const state = await cohortFolders_resolve(read);
     const noted = [];
     if (added > 0)
         noted.push(`${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_wrap(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.
@@ -224,7 +253,7 @@ export async function builtin_gather(args) {
                 if (piped === null) {
                     return gather_error(`gather ${subcommand}: what? give paths or handles (@SER3), \${listing}, or pipe a listing in (query … | gather ${subcommand === 'rm' ? 'remove' : subcommand})`);
                 }
-                given = listingOperands_of(piped) ?? [];
+                given = listingOperands_extract(piped) ?? [];
                 if (given.length === 0)
                     return gather_error(`gather ${subcommand}: the listing piped in has nothing to ${subcommand === 'add' ? 'gather' : 'remove'}.`);
             }
@@ -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

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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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