@fnndsc/brasa 0.45.0 → 0.47.0

package/dist/builtins/res/expect.d.ts

@@ -1,6 +1,8 @@
 import { CommandEnvelope } from '@fnndsc/menu';
 import { duration_parse } from '../../lib/duration.js';
 export { duration_parse };
+import type { ListingItem } from '@fnndsc/menu';
+import { type ExpectAsk, type ExpectReading } from '../../core/backend.js';
 /** The model kind under which a checked claim travels to a surface. */
 export declare const EXPECT_MODEL_KIND: string;
 /** What a claim turned out to be. */
@@ -31,6 +33,42 @@ export declare function claim_holds(got: string, predicate: string, wanted: stri
 } | {
     refusal: string;
 };
+/** How far beneath a named folder a claim will look for what it was asked about. */
+export declare const DEEP_MAX: number;
+/**
+ * Walks a folder, gathering what it holds and the folders under it.
+ *
+ * A plugin's output is routinely NESTED — pfdicom writes under
+ * `share/incoming/<input tree>`, and a converter mirrors its input — so a
+ * claim about what a run produced, made at the node's own folder, would be
+ * false about a run that worked perfectly. The walk is bounded: a claim is
+ * a question about a result, not a crawl of the filesystem.
+ *
+ * @param root - Where to start.
+ * @param depth - How many levels below the root to visit.
+ * @returns Every item found, with the folder each was found in.
+ */
+export declare function folder_walkDeep(root: string, depth: number): Promise<Array<{
+    folder: string;
+    item: ListingItem;
+}>>;
+/** One subject as `expect` sees it: every registration of the name, merged. */
+interface SubjectEntry {
+    named: boolean;
+    /** Each property, with the registration that answers it and the words it takes. */
+    properties: Map<string, {
+        words: number;
+        read: (ask: ExpectAsk) => Promise<ExpectReading>;
+    }>;
+}
+/**
+ * Every subject this session can make claims about: the core's `path`, then
+ * the backend's. Two registrations of one name are one subject, each
+ * answering its own properties (ChRIS adds `tags` to `path`).
+ *
+ * @returns The subjects, by name, in the order they were registered.
+ */
+export declare function expectSubjects_get(): Map<string, SubjectEntry>;
 /**
  * Builtin handler for the `expect` command.
  *

package/dist/builtins/res/expect.js

@@ -2,9 +2,10 @@
  * @file Builtin expect command: a claim the session can refuse.
  *
  * A workflow that only acts is a demonstration. `expect` is what makes one a
- * TEST: it states a claim about the session — how many things are gathered,
- * what a feed's status is, what a produced file's tags say — and refuses,
- * non-zero, when the claim does not hold. Because it is a verb rather than a
+ * TEST: it states a claim about the session — what a path holds, and,
+ * through the subjects a backend registers, how many things are gathered,
+ * what a run's status is, whether a domain verifies — and refuses, non-zero,
+ * when the claim does not hold. Because it is a verb rather than a
  * harness, a workflow asserts wherever it is played: in CI, at an operator's
  * console, or in someone else's browser after they were handed the file.
  *
@@ -13,20 +14,21 @@
  * language has no sleep: a sleep asserts nothing and lies about how long the
  * work actually took.
  *
+ * The grammar, the polling and the verdict are the core's, and so is `path`
+ * (`exists`, `count`). Everything else a claim can be about belongs to a
+ * backend's world, and the backend registers it (`Backend.expectSubjects`):
+ * this file names no backend.
+ *
  * @module
  */
 import chalk from 'chalk';
 import path from 'path';
-import { procCache_get } from '@fnndsc/cumin';
-import { jobs_statusBatch } from '@fnndsc/salsa';
 import { envelope_ok, envelope_error } from '@fnndsc/menu';
 import { commandArgs_process, path_resolve } from '../utils.js';
 import { duration_parse } from '../../lib/duration.js';
 export { duration_parse };
 import { vfs } from '../../lib/vfs/vfs.js';
-import { cohort_read } from './gather.store.js';
-import { path_physical, tagsModel_read } from './dicom.js';
-import { feedStatus_derive } from '../proc.helpers.js';
+import { backendInstalled_get } from '../../core/backend.js';
 import { commandCancellation_enable, commandCancellation_signalGet } from '../../core/cancellation.js';
 /** The model kind under which a checked claim travels to a surface. */
 export const EXPECT_MODEL_KIND = 'expect.result';
@@ -34,8 +36,6 @@ export const EXPECT_MODEL_KIND = 'expect.result';
 const PREDICATES = [
     'eq', 'ne', 'gt', 'gte', 'lt', 'lte', 'contains', 'notContains', 'matches',
 ];
-/** What a claim can be about. */
-const SUBJECTS = ['gather', 'feed', 'run', 'path'];
 /** Predicates that only mean anything about numbers. */
 const NUMERIC_PREDICATES = new Set(['gt', 'gte', 'lt', 'lte']);
 /** How often a waiting claim asks again. */
@@ -82,79 +82,8 @@ export function claim_holds(got, predicate, wanted) {
         return { refusal: `matches needs a regular expression, and "${wanted}" is not one` };
     }
 }
-/**
- * Reads how much of the cohort is home.
- *
- * A place gathered from the filesystem was never anywhere else, so it counts
- * as home; a series counts once CUBE has said where it landed.
- *
- * @param state - The cohort.
- * @returns How many members are in CUBE.
- */
-function cohortPulled_count(state) {
-    return state.series.filter((member) => {
-        if (member.kind !== 'series')
-            return true;
-        const landed = member.folderPath;
-        return typeof landed === 'string' && landed.length > 0;
-    }).length;
-}
-/**
- * Answers a claim about the cohort.
- *
- * @param property - `size` or `pulled`.
- * @returns What the cohort says.
- */
-async function gather_read(property) {
-    const state = await cohort_read();
-    if (property === 'size')
-        return { got: `${state.series.length}` };
-    if (property === 'pulled')
-        return { got: `${cohortPulled_count(state)}` };
-    if (property === 'name')
-        return { got: state.name ?? '' };
-    return { got: null, refusal: `gather has no property "${property}" — try size, pulled or name` };
-}
-/**
- * Answers a claim about a feed.
- *
- * @param target - The feed id.
- * @param property - `status` today.
- * @returns What the feed says.
- */
-async function feed_read(target, property) {
-    const feedID = Number(target);
-    if (!Number.isInteger(feedID))
-        return { got: null, refusal: `"${target}" is not a feed id` };
-    if (property !== 'status')
-        return { got: null, refusal: `feed has no property "${property}" — try status` };
-    const feed = procCache_get().feed_get(feedID);
-    if (feed === undefined || feed === null) {
-        return { got: null, refusal: `feed ${feedID} is not in this session's index yet` };
-    }
-    return { got: feedStatus_derive(feed) };
-}
-/**
- * Answers a claim about one run.
- *
- * @param target - The plugin instance id.
- * @param property - `status` today.
- * @returns What the run says.
- */
-async function run_read(target, property) {
-    const instanceID = Number(target);
-    if (!Number.isInteger(instanceID))
-        return { got: null, refusal: `"${target}" is not an instance id` };
-    if (property !== 'status')
-        return { got: null, refusal: `run has no property "${property}" — try status` };
-    const statuses = await jobs_statusBatch([instanceID]);
-    const status = statuses.get(instanceID);
-    if (status === undefined)
-        return { got: null, refusal: `instance ${instanceID} did not answer` };
-    return { got: status };
-}
 /** How far beneath a named folder a claim will look for what it was asked about. */
-const DEEP_MAX = 4;
+export const DEEP_MAX = 4;
 /**
  * Walks a folder, gathering what it holds and the folders under it.
  *
@@ -168,7 +97,7 @@ const DEEP_MAX = 4;
  * @param depth - How many levels below the root to visit.
  * @returns Every item found, with the folder each was found in.
  */
-async function folder_walkDeep(root, depth) {
+export async function folder_walkDeep(root, depth) {
     const found = [];
     const queue = [{ path: root, level: 0 }];
     while (queue.length > 0) {
@@ -198,19 +127,14 @@ function glob_toRegExp(pattern) {
     return new RegExp(`^${escaped}$`);
 }
 /**
- * Answers a claim about a path: whether it is there, what it holds, what its
- * headers say.
+ * Answers a claim about a path: whether it is there, and what it holds.
  *
- * @param target - The path, as the operator wrote it.
- * @param property - `exists`, `count`, or `tags`.
- * @param tagName - The tag to read, when the property is `tags`.
- * @param matching - A glob narrowing a count.
- * @param deep - Look beneath the folder, not only in it.
+ * @param ask - The claim, as the path subject is asked it.
  * @returns What the path says.
  */
-async function path_read(target, property, tagName, matching, deep) {
-    const resolved = await path_resolve(target);
-    if (property === 'exists') {
+async function path_read(ask) {
+    const resolved = await path_resolve(ask.target ?? '');
+    if (ask.property === 'exists') {
         const listed = await vfs.data_get(resolved);
         if (listed.ok)
             return { got: 'true' };
@@ -221,85 +145,43 @@ async function path_read(target, property, tagName, matching, deep) {
         const leaf = path.posix.basename(resolved);
         return { got: `${parent.value.some((item) => item.name === leaf)}` };
     }
-    if (property === 'count') {
-        if (deep) {
-            const walked = await folder_walkDeep(resolved, DEEP_MAX);
-            const files = walked
-                .map((entry) => entry.item)
-                .filter((item) => item.type !== 'dir');
-            if (matching === undefined)
-                return { got: `${files.length}` };
-            const deepPattern = glob_toRegExp(matching);
-            return { got: `${files.filter((item) => deepPattern.test(item.name)).length}` };
-        }
-        const listed = await vfs.data_get(resolved);
-        if (!listed.ok)
-            return { got: null, refusal: `${resolved} cannot be listed` };
-        if (matching === undefined)
-            return { got: `${listed.value.length}` };
-        const pattern = glob_toRegExp(matching);
-        return { got: `${listed.value.filter((item) => pattern.test(item.name)).length}` };
+    if (ask.deep) {
+        const walked = await folder_walkDeep(resolved, DEEP_MAX);
+        const files = walked
+            .map((entry) => entry.item)
+            .filter((item) => item.type !== 'dir');
+        if (ask.matching === undefined)
+            return { got: `${files.length}` };
+        const deepPattern = glob_toRegExp(ask.matching);
+        return { got: `${files.filter((item) => deepPattern.test(item.name)).length}` };
     }
-    if (property === 'tags') {
-        if (tagName === undefined)
-            return { got: null, refusal: 'expect path <p> tags <TagName> <predicate> <value>' };
-        const physical = await path_physical(resolved);
-        let model = await tagsModel_read(physical);
-        if (!model.ok) {
-            // A plugin's output is routinely nested, so a tag claim made at the
-            // node's own folder looks BENEATH it before giving up: the files a run
-            // produced are what the claim is about, wherever the plugin filed them.
-            const walked = await folder_walkDeep(resolved, DEEP_MAX);
-            const folders = [...new Set(walked
-                    .filter((entry) => entry.item.type === 'dir')
-                    .map((entry) => `${entry.folder.replace(/\/$/, '')}/${entry.item.name}`))];
-            for (const folder of folders) {
-                const beneath = await tagsModel_read(await path_physical(folder));
-                if (beneath.ok) {
-                    model = beneath;
-                    break;
-                }
-            }
-        }
-        if (!model.ok)
-            return { got: null, refusal: `${resolved} holds no readable DICOM, here or beneath it` };
-        const constant = model.value.constant.find((tag) => tag.name === tagName || tag.tag === tagName);
-        if (constant !== undefined)
-            return { got: constant.value };
-        // A tag that varies across the folder answers with every value it takes,
-        // so a claim about "the" value cannot pass by reading only the first file.
-        const varying = model.value.varying.find((tag) => tag.name === tagName || tag.tag === tagName);
-        if (varying !== undefined) {
-            const values = [...new Set(varying.values
-                    .map((entry) => entry.value ?? '')
-                    .filter((value) => value.length > 0))];
-            return { got: values.join(', ') };
-        }
-        return { got: '' };
-    }
-    return { got: null, refusal: `path has no property "${property}" — try exists, count or tags` };
+    const listed = await vfs.data_get(resolved);
+    if (!listed.ok)
+        return { got: null, refusal: `${resolved} cannot be listed` };
+    if (ask.matching === undefined)
+        return { got: `${listed.value.length}` };
+    const pattern = glob_toRegExp(ask.matching);
+    return { got: `${listed.value.filter((item) => pattern.test(item.name)).length}` };
 }
+/** The core's own subject: a path in the session's filesystem. */
+const PATH_SUBJECT = { name: 'path', named: true, properties: { exists: 0, count: 0 }, read: path_read };
 /**
- * Asks the session once.
+ * Every subject this session can make claims about: the core's `path`, then
+ * the backend's. Two registrations of one name are one subject, each
+ * answering its own properties (ChRIS adds `tags` to `path`).
  *
- * @param subject - What the claim is about.
- * @param target - Which one, for the subjects that need naming.
- * @param property - What about it.
- * @param tagName - The tag, when the property is `tags`.
- * @param matching - A glob, when the property is `count`.
- * @param deep - Whether to look beneath the path as well as in it.
- * @returns What the session answered.
+ * @returns The subjects, by name, in the order they were registered.
  */
-async function subject_read(subject, target, property, tagName, matching, deep) {
-    if (subject === 'gather')
-        return await gather_read(property);
-    if (subject === 'feed')
-        return await feed_read(target ?? '', property);
-    if (subject === 'run')
-        return await run_read(target ?? '', property);
-    if (subject === 'path')
-        return await path_read(target ?? '', property, tagName, matching, deep);
-    return { got: null, refusal: `expect knows nothing about "${subject}" — try gather, feed, run or path` };
+export function expectSubjects_get() {
+    const subjects = new Map();
+    for (const subject of [PATH_SUBJECT, ...(backendInstalled_get()?.expectSubjects ?? [])]) {
+        const entry = subjects.get(subject.name) ?? { named: subject.named, properties: new Map() };
+        for (const [property, words] of Object.entries(subject.properties)) {
+            entry.properties.set(property, { words, read: subject.read });
+        }
+        subjects.set(subject.name, entry);
+    }
+    return subjects;
 }
 /**
  * Sleeps between asks, unless the command is cancelled first.
@@ -341,27 +223,36 @@ export async function builtin_expect(args) {
     const parsed = commandArgs_process(args, { booleanLongOptions: ['deep'] });
     const operands = parsed._;
     const subject = operands[0];
+    const subjects = expectSubjects_get();
+    const names = [...subjects.keys()].join(', ');
     if (subject === undefined) {
         process.exitCode = 1;
-        return envelope_error('', undefined, `${chalk.red('Usage: expect <gather|feed|run|path> [<target>] <property> [<predicate> <value>] [--within <duration>]')}\n`);
+        return envelope_error('', undefined, `${chalk.red(`Usage: expect <${[...subjects.keys()].join('|')}> [<target>] <property> [<predicate> <value>] [--within <duration>]`)}\n`);
     }
     // The subject is checked FIRST: read as a shape instead, an unknown
     // subject refuses by complaining about whatever word happened to land
     // where a comparison goes, which names the wrong fault.
-    if (!SUBJECTS.includes(subject)) {
+    const entry = subjects.get(subject);
+    if (entry === undefined) {
         process.exitCode = 1;
-        return envelope_error('', undefined, `${chalk.red(`expect knows nothing about "${subject}" — try ${SUBJECTS.join(', ')}.`)}\n`);
+        return envelope_error('', undefined, `${chalk.red(`expect knows nothing about "${subject}" in this session — try ${names}.`)}\n`);
     }
-    // `gather` is the one subject that names nothing: there is one cohort.
-    const named = subject !== 'gather';
-    const target = named ? operands[1] : undefined;
-    const property = named ? operands[2] : operands[1];
-    const rest = named ? operands.slice(3) : operands.slice(2);
-    const tagName = property === 'tags' ? rest.shift() : undefined;
+    // A subject that is one thing (`gather`: there is one cohort) names nothing.
+    const target = entry.named ? operands[1] : undefined;
+    const property = entry.named ? operands[2] : operands[1];
+    const rest = entry.named ? operands.slice(3) : operands.slice(2);
+    const properties = [...entry.properties.keys()].join(', ');
     if (property === undefined) {
         process.exitCode = 1;
-        return envelope_error('', undefined, `${chalk.red(`expect ${subject}: say what about it — a property such as size, status, exists or count.`)}\n`);
+        return envelope_error('', undefined, `${chalk.red(`expect ${subject}: say what about it — ${properties}.`)}\n`);
+    }
+    const answering = entry.properties.get(property);
+    if (answering === undefined) {
+        process.exitCode = 1;
+        return envelope_error('', undefined, `${chalk.red(`expect: ${subject} has no property "${property}" — try ${properties}.`)}\n`);
     }
+    // A property may take words before the comparison (`tags PatientID`).
+    const words = rest.splice(0, answering.words);
     // `expect path <p> exists` is the claim in full; everything else compares.
     const predicate = rest[0] ?? (property === 'exists' ? 'eq' : '');
     const wanted = rest[1] ?? (property === 'exists' ? 'true' : '');
@@ -383,17 +274,24 @@ export async function builtin_expect(args) {
     // held, and a battery is read by people who were not there.
     const narrowing = matching_get(parsed) === undefined ? '' : `--matching '${matching_get(parsed)}'`;
     const claim = claim_render([
-        subject, target ?? '', property, tagName ?? '', narrowing,
+        subject, target ?? '', property, ...words, narrowing,
         parsed.deep === true ? '--deep' : '', predicate, wanted,
     ]);
     const started = Date.now();
     if (deadlineMs > 0)
         commandCancellation_enable();
     const signal = deadlineMs > 0 ? commandCancellation_signalGet() : undefined;
+    const matching = matching_get(parsed);
     let reading = { got: null };
     let outcome = { held: false };
     for (;;) {
-        reading = await subject_read(subject, target, property, tagName, matching_get(parsed), parsed.deep === true);
+        reading = await answering.read({
+            ...(target !== undefined ? { target } : {}),
+            property,
+            words,
+            ...(matching !== undefined ? { matching } : {}),
+            deep: parsed.deep === true,
+        });
         if (reading.got !== null) {
             outcome = claim_holds(reading.got, predicate, wanted);
             if ('refusal' in outcome)

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

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

@@ -1,6 +1,6 @@
 import { CommandEnvelope } from '@fnndsc/menu';
-/** The model kind under which a cohort travels to a surface. */
-export declare const GATHER_MODEL_KIND: string;
+import { GATHER_MODEL_KIND } from './gather.kind.js';
+export { GATHER_MODEL_KIND };
 /**
  * Builtin handler for the `gather` command.
  *

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_of(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_of(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_of(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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