@fnndsc/salsa 3.8.1 → 3.10.0

package/dist/pipelines/packages.js

@@ -0,0 +1,181 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pipelinePackagesPath_get = pipelinePackagesPath_get;
+exports.pipelinePackages_restore = pipelinePackages_restore;
+exports.pipelinePackages_sweep = pipelinePackages_sweep;
+exports.pipelinePackages_all = pipelinePackages_all;
+exports.pipelinePackage_find = pipelinePackage_find;
+/**
+ * @file The pipeline package store: durable pre-cache of registered pipelines.
+ *
+ * A registered pipeline is immutable, so what CUBE knows about it — identity
+ * fields and the complete registered manifest — is fetched once, held in
+ * memory, and checkpointed to a local file keyed by the CUBE URL. The sweep
+ * runs as a warm-up tail after the topology index settles: it lists the
+ * registry and fetches only pipelines the store has never seen, so the
+ * steady-state cost is zero and a fresh daemon restores everything without
+ * a wire call. The `/usr/share/packages/<pipeline>` VFS tree and the diagram
+ * builder both read from here.
+ *
+ * @module
+ */
+const crypto_1 = require("crypto");
+const fs_1 = require("fs");
+const os_1 = require("os");
+const path_1 = require("path");
+const cumin_1 = require("@fnndsc/cumin");
+const manifest_js_1 = require("./manifest.js");
+const index_js_1 = require("../context/index.js");
+/** Bumped when the persisted shape changes; older files are ignored. */
+const PACKAGES_SCHEMA = 1;
+/** The in-memory store, keyed by pipeline id. */
+const packages = new Map();
+/** The CUBE key the store was restored for; a different CUBE resets it. */
+let restoredKey = null;
+/** Returns the default directory for persistent pipeline-package files. */
+function packagesRoot_get() {
+    const cacheHome = process.env['XDG_CACHE_HOME'] ?? (0, path_1.join)((0, os_1.homedir)(), '.cache');
+    return (0, path_1.join)(cacheHome, 'chell', 'pipelines');
+}
+/**
+ * Builds the CUBE-keyed store path without exposing the URL.
+ *
+ * @param cubeUrl - The CUBE API URL the registry belongs to.
+ * @param root - Store directory override (tests).
+ * @returns Versioned store file path.
+ */
+function pipelinePackagesPath_get(cubeUrl, root = packagesRoot_get()) {
+    const key = (0, crypto_1.createHash)('sha256').update(cubeUrl).digest('hex').slice(0, 16);
+    return (0, path_1.join)(root, `packages-${key}-v${PACKAGES_SCHEMA}.json`);
+}
+/** Resolves the current CUBE's store key, or null when disconnected. */
+async function storeKey_get() {
+    try {
+        const context = await (0, index_js_1.context_getSingle)();
+        return context.URL ?? null;
+    }
+    catch {
+        return null;
+    }
+}
+/** Structurally validates one persisted package entry. */
+function package_check(value) {
+    if (!value || typeof value !== 'object')
+        return false;
+    const entry = value;
+    return typeof entry.id === 'number' &&
+        typeof entry.name === 'string' &&
+        typeof entry.manifest === 'object' && entry.manifest !== null &&
+        Array.isArray(entry.manifest.nodes) &&
+        Array.isArray(entry.manifest.rootIDs);
+}
+/**
+ * Restores the store from its durable file for the current CUBE, once per
+ * key. Missing or invalid files leave the store empty — the sweep refills.
+ *
+ * @param root - Store directory override (tests).
+ */
+async function pipelinePackages_restore(root = packagesRoot_get()) {
+    const key = await storeKey_get();
+    if (key === null || key === restoredKey)
+        return;
+    restoredKey = key;
+    packages.clear();
+    try {
+        const raw = await fs_1.promises.readFile(pipelinePackagesPath_get(key, root), 'utf8');
+        const parsed = JSON.parse(raw);
+        const entries = parsed.packages;
+        if (!Array.isArray(entries))
+            return;
+        for (const entry of entries) {
+            if (package_check(entry))
+                packages.set(entry.id, entry);
+        }
+    }
+    catch {
+        // No file yet, or an unreadable one: the sweep rebuilds it.
+    }
+}
+/**
+ * Writes the store durably, atomically, keyed by the current CUBE.
+ *
+ * @param key - The CUBE URL key.
+ * @param root - Store directory override (tests).
+ */
+async function packages_save(key, root = packagesRoot_get()) {
+    const path = pipelinePackagesPath_get(key, root);
+    const temporaryPath = `${path}.${process.pid}.tmp`;
+    const file = {
+        schema: PACKAGES_SCHEMA,
+        savedAt: new Date().toISOString(),
+        packages: Array.from(packages.values()),
+    };
+    await fs_1.promises.mkdir((0, path_1.dirname)(path), { recursive: true, mode: 0o700 });
+    await fs_1.promises.writeFile(temporaryPath, `${JSON.stringify(file)}\n`, { encoding: 'utf8', mode: 0o600 });
+    await fs_1.promises.rename(temporaryPath, path);
+}
+/**
+ * The warm-up tail: lists the registry and fetches manifests only for
+ * pipelines the store has never seen, then saves. Sequential awaits are the
+ * throttle; per-pipeline failures are skipped and retried next sweep.
+ *
+ * @param root - Store directory override (tests).
+ */
+async function pipelinePackages_sweep(root = packagesRoot_get()) {
+    const key = await storeKey_get();
+    if (key === null)
+        return;
+    await pipelinePackages_restore(root);
+    const listed = await (0, cumin_1.pipelines_list)();
+    if (!listed.ok)
+        return;
+    const client = await cumin_1.chrisConnection.client_get();
+    if (!client)
+        return;
+    let added = false;
+    for (const record of listed.value) {
+        if (packages.has(record.id))
+            continue;
+        const handle = await (0, cumin_1.pipeline_get)(client, record.id);
+        if (!handle)
+            continue;
+        const manifest = await (0, manifest_js_1.pipelineManifestForPipeline_get)(record, handle, { detail: 'registered' });
+        if (!manifest.ok)
+            continue;
+        packages.set(record.id, {
+            id: record.id,
+            name: record.name,
+            ...(typeof record.slug === 'string' ? { slug: record.slug } : {}),
+            ...(typeof record.authors === 'string' ? { authors: record.authors } : {}),
+            ...(typeof record.category === 'string' ? { category: record.category } : {}),
+            ...(typeof record.description === 'string' ? { description: record.description } : {}),
+            ...(typeof record.locked === 'boolean' ? { locked: record.locked } : {}),
+            manifest: manifest.value,
+        });
+        added = true;
+    }
+    if (added)
+        await packages_save(key, root);
+}
+/** @returns Every cached package, sorted by name. */
+function pipelinePackages_all() {
+    return Array.from(packages.values()).sort((a, b) => a.name.localeCompare(b.name));
+}
+/**
+ * Finds one cached package by id, exact name, or slug.
+ *
+ * @param specifier - Pipeline id (digits), name, or slug.
+ * @returns The package, or null when the store holds no match.
+ */
+function pipelinePackage_find(specifier) {
+    const trimmed = specifier.trim();
+    if (/^\d+$/.test(trimmed)) {
+        return packages.get(parseInt(trimmed, 10)) ?? null;
+    }
+    for (const entry of packages.values()) {
+        if (entry.name === trimmed || entry.slug === trimmed)
+            return entry;
+    }
+    return null;
+}
+//# sourceMappingURL=packages.js.map

package/dist/pipelines/packages.js.map

@@ -0,0 +1 @@
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package/dist/retrieve/watch.d.ts

@@ -1,6 +1,15 @@
 import { type Client } from '@fnndsc/cumin';
-/** Lifecycle states of one series retrieve. */
-export type RetrieveStatus = 'pending' | 'pulling' | 'pulled' | 'stalled' | 'timeout' | 'error' | 'unfired';
+/**
+ * Lifecycle states of one series retrieve.
+ *
+ * `unconfirmed` is the state of a series the client stopped watching before it
+ * could see the end. It is not a failure: the PACS keeps pushing and CUBE keeps
+ * registering after a watch ends, so the retrieve is very likely still running
+ * or already done. Reporting such a series as `error` claims knowledge the
+ * client does not have, and a caller that treats it as failure will tell an
+ * operator that nothing arrived while the files land behind them.
+ */
+export type RetrieveStatus = 'pending' | 'pulling' | 'pulled' | 'stalled' | 'timeout' | 'error' | 'unfired' | 'unconfirmed';
 /** Progress classification reported to event consumers. */
 export type RetrieveProgressStatus = 'running' | 'done' | 'unconfirmed' | 'error' | 'stalled' | 'timeout';
 /**
@@ -46,6 +55,11 @@ export interface RetrieveTask {
 export interface RetrieveWatchEvents {
     task?: (task: RetrieveTask, status: RetrieveProgressStatus, phase: 'watching' | 'retrying') => void;
     retryRound?: (attempt: number, retryMax: number, count: number) => void;
+    /**
+     * The watch socket dropped and is being reopened. Reported because a silent
+     * reconnection during a long pull looks identical to a stall.
+     */
+    reconnect?: (attempt: number, maxAttempts: number, watching: number) => void;
 }
 /**
  * Builds a fresh retrieve task from series identity facts.

package/dist/retrieve/watch.js

@@ -35,6 +35,14 @@ const FIRE_CONCURRENCY = 4;
 /** Retry attempts for one retrieve creation, with backoff between them. */
 const FIRE_ATTEMPTS = 3;
 const FIRE_BACKOFF_MS = [250, 500];
+/**
+ * Reconnection attempts for a dropped LONK socket.
+ *
+ * A long retrieve gives a socket more chances to die, which is why a large
+ * study failed where a small one did not. The retrieves are unaffected by the
+ * loss, so reconnecting resumes reporting rather than repeating work.
+ */
+const WATCH_RECONNECT_ATTEMPTS = 3;
 const STALL_TIMEOUT_MS = 30_000;
 const NO_ACTIVITY_TIMEOUT_MS = 15_000;
 const SERIES_TIMEOUT_MS = 5 * 60 * 1_000;
@@ -194,14 +202,26 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
         events.task?.(task, status ?? retrieveProgress_classify(task), phase);
     };
     const downloadToken = await (0, cumin_1.downloadToken_create)(client);
-    const ws = new ws_1.default(lonkWsUrl_build(downloadToken.url, downloadToken.token));
-    await new Promise((openResolve, openReject) => {
-        ws.once('open', openResolve);
-        ws.once('error', (err) => openReject(err));
-    });
-    for (const t of tasks) {
-        ws.send(JSON.stringify({ SeriesInstanceUID: t.seriesUID, pacs_name: t.pacsName, action: 'subscribe' }));
-    }
+    const lonkUrl = lonkWsUrl_build(downloadToken.url, downloadToken.token);
+    /**
+     * Opens a LONK socket and subscribes it to the series given.
+     *
+     * A reconnect subscribes only what is still in flight: the retrieves are
+     * already running on the server, so re-firing them would duplicate work that
+     * was never lost.
+     */
+    const socket_open = async (subscribe) => {
+        const socket = new ws_1.default(lonkUrl);
+        await new Promise((openResolve, openReject) => {
+            socket.once('open', openResolve);
+            socket.once('error', (err) => openReject(err));
+        });
+        for (const t of subscribe) {
+            socket.send(JSON.stringify({ SeriesInstanceUID: t.seriesUID, pacs_name: t.pacsName, action: 'subscribe' }));
+        }
+        return socket;
+    };
+    let ws = await socket_open(tasks);
     await tasks_fireBounded(tasks, pacsserver);
     const fired = tasks.filter((t) => t.status !== 'unfired');
     const firingErrors = tasks.length - fired.length;
@@ -219,6 +239,7 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
     const taskByUID = new Map(tasks.map((t) => [t.seriesUID, t]));
     await new Promise((resolve) => {
         let resolved = false;
+        let reconnectsLeft = WATCH_RECONNECT_ATTEMPTS;
         const done = () => {
             if (resolved)
                 return;
@@ -230,11 +251,54 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
             catch { /* best-effort socket cleanup */ }
             resolve();
         };
+        /** The series this watch is still waiting on. */
+        const inFlight = () => fired.filter((t) => t.status === 'pending' || t.status === 'pulling');
+        /**
+         * Replaces a dead socket, or gives up and records what is unknown.
+         *
+         * A LONK socket carries no state a client cannot rebuild: the retrieves run
+         * on the server regardless, and a fresh subscription resumes reporting on
+         * them. Only when reconnection is exhausted does the watch admit it stopped
+         * looking — and even then it says so rather than calling the retrieves
+         * failed.
+         */
+        const socket_replace = () => {
+            if (resolved)
+                return;
+            const remaining = inFlight();
+            if (remaining.length === 0) {
+                done();
+                return;
+            }
+            if (reconnectsLeft <= 0) {
+                for (const t of remaining) {
+                    t.status = 'unconfirmed';
+                    emit(t, 'unconfirmed');
+                }
+                done();
+                return;
+            }
+            reconnectsLeft -= 1;
+            events.reconnect?.(WATCH_RECONNECT_ATTEMPTS - reconnectsLeft, WATCH_RECONNECT_ATTEMPTS, remaining.length);
+            void socket_open(remaining)
+                .then((replacement) => {
+                if (resolved) {
+                    try {
+                        replacement.close();
+                    }
+                    catch { /* the watch already ended */ }
+                    return;
+                }
+                ws = replacement;
+                socket_listen();
+            })
+                .catch(() => socket_replace());
+        };
         const checker = setInterval(() => {
             const now = Date.now();
             let allTerminal = true;
             for (const t of fired) {
-                if (t.status === 'pulled' || t.status === 'error' || t.status === 'unfired' || t.status === 'stalled' || t.status === 'timeout') {
+                if (t.status === 'pulled' || t.status === 'error' || t.status === 'unfired' || t.status === 'stalled' || t.status === 'timeout' || t.status === 'unconfirmed') {
                     continue;
                 }
                 allTerminal = false;
@@ -258,52 +322,51 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
             if (allTerminal)
                 done();
         }, CHECKER_INTERVAL_MS);
-        ws.on('message', (data) => {
-            try {
-                const outer = JSON.parse(data.toString());
-                const seriesUID = outer.SeriesInstanceUID;
-                const message = outer.message;
-                if (!seriesUID || !message)
-                    return;
-                const t = taskByUID.get(seriesUID);
-                if (!t)
-                    return;
-                if ('ndicom' in message && typeof message.ndicom === 'number') {
-                    const n = message.ndicom;
-                    t.actualFiles = n;
-                    t.lastProgressFiles = n;
-                    t.lastProgressTime = Date.now();
-                    if (t.status === 'pending')
-                        t.status = 'pulling';
-                    emit(t, 'running');
-                }
-                else if ('done' in message && message.done === true) {
-                    t.status = 'pulled';
-                    t.lonkConfirmed = true;
-                    if (t.actualFiles < t.expectedFiles)
-                        t.actualFiles = t.expectedFiles;
-                    emit(t, 'done');
+        /** Attaches this watch's handlers to whichever socket is current. */
+        const socket_listen = () => {
+            ws.on('message', (data) => {
+                try {
+                    const outer = JSON.parse(data.toString());
+                    const seriesUID = outer.SeriesInstanceUID;
+                    const message = outer.message;
+                    if (!seriesUID || !message)
+                        return;
+                    const t = taskByUID.get(seriesUID);
+                    if (!t)
+                        return;
+                    if ('ndicom' in message && typeof message.ndicom === 'number') {
+                        const n = message.ndicom;
+                        t.actualFiles = n;
+                        t.lastProgressFiles = n;
+                        t.lastProgressTime = Date.now();
+                        if (t.status === 'pending')
+                            t.status = 'pulling';
+                        emit(t, 'running');
+                    }
+                    else if ('done' in message && message.done === true) {
+                        t.status = 'pulled';
+                        t.lonkConfirmed = true;
+                        if (t.actualFiles < t.expectedFiles)
+                            t.actualFiles = t.expectedFiles;
+                        emit(t, 'done');
+                    }
+                    else if ('error' in message && typeof message.error === 'string') {
+                        t.status = 'error';
+                        emit(t, 'error');
+                    }
                 }
-                else if ('error' in message && typeof message.error === 'string') {
-                    t.status = 'error';
-                    emit(t, 'error');
+                catch {
+                    // Deliberate absorption: a malformed LONK frame carries no correlation
+                    // to fail; the checker's stall/timeout guards still bound the watch.
                 }
-            }
-            catch {
-                // Deliberate absorption: a malformed LONK frame carries no correlation
-                // to fail; the checker's stall/timeout guards still bound the watch.
-            }
-        });
-        ws.on('error', () => {
-            for (const t of fired) {
-                if (t.status === 'pending' || t.status === 'pulling') {
-                    t.status = 'error';
-                    emit(t, 'error');
-                }
-            }
-            done();
-        });
-        ws.on('close', () => { done(); });
+            });
+            // A dead socket is a lost view, not a lost retrieve: reconnect and keep
+            // watching. Only when that fails repeatedly does the watch stop, and even
+            // then it records what it no longer knows rather than declaring failure.
+            ws.on('error', () => { socket_replace(); });
+            ws.on('close', () => { socket_replace(); });
+        };
+        socket_listen();
     });
     return firingErrors;
 }
@@ -322,13 +385,20 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
  */
 async function retrieve_confirmLoop(allTasks, retryMax, pacsserver, client, events = {}) {
     let extraFiringErrors = 0;
-    let retryCandidates = allTasks.filter((t) => t.status === 'pulled' && !t.lonkConfirmed);
+    // A series the watch lost sight of is a candidate for exactly the same
+    // treatment as one whose confirmation went missing: ask CUBE. Both are
+    // "we did not see the end", and CUBE is the only thing that knows.
+    let retryCandidates = allTasks.filter((t) => (t.status === 'pulled' && !t.lonkConfirmed) || t.status === 'unconfirmed');
     for (let attempt = 1; attempt <= retryMax && retryCandidates.length > 0; attempt++) {
         await Promise.all(retryCandidates.map(async (t) => {
             const stateResult = await (0, cumin_1.seriesStorage_resolve)(t.seriesUID);
             if (stateResult.ok && stateResult.value.folderPath !== null) {
                 t.lonkConfirmed = true;
                 t.cubePathDir = stateResult.value.folderPath;
+                // A series found in CUBE arrived, whatever the watch managed to see.
+                t.status = 'pulled';
+                t.actualFiles = stateResult.value.fileCount;
+                events.task?.(t, 'done', 'retrying');
             }
         }));
         retryCandidates = retryCandidates.filter((t) => !t.lonkConfirmed);

package/dist/retrieve/watch.js.map

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package/dist/vfs/dispatcher.js

@@ -14,6 +14,9 @@ const native_js_1 = require("./providers/native.js");
 const pacs_js_1 = require("./providers/pacs.js");
 const etc_js_1 = require("./providers/etc.js");
 const proc_js_1 = require("./providers/proc.js");
+const workflows_js_1 = require("./providers/workflows.js");
+const tags_js_1 = require("./providers/tags.js");
+const share_js_1 = require("./providers/share.js");
 /**
  * Registry and dispatcher routing filesystem commands to matched VFS providers.
  */
@@ -29,6 +32,12 @@ class VFSDispatcher {
         this.provider_register(new pacs_js_1.PacsVfsProvider());
         this.provider_register(new etc_js_1.EtcVfsProvider());
         this.provider_register(new proc_js_1.ProcVfsProvider());
+        // Three relations CUBE owns and the namespace did not reach: the tags a
+        // feed can carry, the runs a pipeline produced, and what is known about a
+        // plugin as opposed to how to invoke it.
+        this.provider_register(new workflows_js_1.WorkflowsVfsProvider());
+        this.provider_register(new tags_js_1.TagsVfsProvider());
+        this.provider_register(new share_js_1.ShareVfsProvider());
     }
     /**
      * Registers a path resolution hook that maps logical paths to physical paths.

package/dist/vfs/dispatcher.js.map

@@ -1 +1 @@
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package/dist/vfs/providers/pacsGrammar.d.ts

@@ -0,0 +1,69 @@
+/**
+ * @file The PACS VFS folder grammar, both directions.
+ *
+ * Query folders are named `<desc>_qid:<id>[_<user>][_no-hits]`, study
+ * folders `Study_<uid>_<desc>`, series folders `Series_<uid>_<desc>`. This
+ * module owns building those names and parsing them back, so a path a
+ * surface builds is always the path the listing shows.
+ *
+ * Deliberately dependency-free: test mocks forward these functions directly
+ * (via the package's `./pacs-grammar` subpath export) instead of maintaining
+ * copies, so nothing here may import anything.
+ *
+ * @module
+ */
+/**
+ * Extracts the numeric query id from a query folder name or any path
+ * containing one.
+ *
+ * @param folder - Folder name or full path carrying a `_qid:<id>` marker.
+ * @returns The query id, or NaN when no marker is present.
+ */
+export declare function queryId_extractFromFolder(folder: string): number;
+/**
+ * Extracts the descriptive label of a query folder, the part before its
+ * `_qid:` marker (the id, user, and no-hits suffixes are all dropped).
+ *
+ * @param folder - Query folder name (`<desc>_qid:<id>[_<user>][_no-hits]`).
+ * @returns The label, or the folder unchanged when it carries no marker.
+ */
+export declare function queryLabel_extractFromFolder(folder: string): string;
+/**
+ * Extracts the UID portion of a study or series folder name
+ * (`<prefix>_<uid>_<label>`).
+ *
+ * @param folder - The folder name.
+ * @param prefix - The expected prefix, `Study` or `Series`.
+ * @returns The UID between the prefix and the first following underscore.
+ */
+export declare function folderUID_get(folder: string, prefix: string): string;
+/**
+ * Everything that determines a query folder's name.
+ *
+ * @property queryId - The query's numeric id.
+ * @property queryObj - The query's key-value search terms; blank values are
+ *   skipped.
+ * @property title - The query record's title, used as the description when
+ *   queryObj yields nothing.
+ * @property username - Owning username, appended as `_<user>` when present.
+ * @property hasResult - Whether the query holds a result payload; false
+ *   appends the `_no-hits` suffix. Defaults to true.
+ */
+export interface QueryFolderNameParts {
+    queryId: number | string;
+    queryObj: Record<string, unknown>;
+    title?: string;
+    username?: string;
+    hasResult?: boolean;
+}
+/**
+ * Builds a query folder name: `<desc>_qid:<id>[_<user>][_no-hits]`.
+ *
+ * This is the single naming authority: the listing provider and any surface
+ * that pre-computes a query's path must both use it, otherwise a freshly
+ * created query can be addressed by a name `ls` will never show.
+ *
+ * @param parts - The name's inputs. See QueryFolderNameParts.
+ * @returns The folder name (no leading path).
+ */
+export declare function queryFolderName_build(parts: QueryFolderNameParts): string;