@fnndsc/salsa 3.9.0 → 3.10.0

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/proc.d.ts

@@ -37,6 +37,12 @@ export declare function procPath_parse(pathStr: string): {
     feedID: number | null;
     instanceID: number | null;
     virtualFile: string | null;
+    /**
+     * Set when the path descends THROUGH an instance's `data` link: the
+     * portion after `data`, '' for the link itself. Everything under the
+     * link belongs to the link's CFS target, not to `/proc`.
+     */
+    dataRemainder: string | null;
 };
 /**
  * VFS provider exposing running jobs and feeds under the /proc namespace.
@@ -56,6 +62,14 @@ export declare class ProcVfsProvider implements VFSProvider {
         sort?: 'name' | 'size' | 'date' | 'owner';
         reverse?: boolean;
     }): Promise<Result<VFSItem[]>>;
+    /**
+     * Binary bytes exist only under the `data` link (an image in a job's
+     * output space); everything else in `/proc` is synthesized text.
+     *
+     * @param pathStr - Absolute `/proc/jobs/.../data/...` path.
+     * @returns The target file's bytes.
+     */
+    readBinary(pathStr: string): Promise<Result<Buffer>>;
     read(pathStr: string): Promise<Result<string>>;
     rm(pathStr: string, _options?: {
         recursive?: boolean;

package/dist/vfs/providers/proc.js

@@ -28,6 +28,8 @@ exports.procTopology_await = procTopology_await;
 exports.procCache_refresh = procCache_refresh;
 const cumin_1 = require("@fnndsc/cumin");
 const index_js_1 = require("../../jobs/index.js");
+const feedJoins_js_1 = require("../../dag/feedJoins.js");
+const packages_js_1 = require("../../pipelines/packages.js");
 /** Virtual filenames inside each instance directory. */
 const INSTANCE_FILES = new Set(['status', 'params', 'log', 'data']);
 /** Virtual filenames inside each feed directory. */
@@ -94,6 +96,14 @@ async function cache_ensure() {
  * Loads instance topology for a single feed.
  * Uses in-flight map to prevent duplicate API calls.
  */
+/** Pulls the execution metrics a CUBE list row carries, defined-only. */
+function instanceMetrics_fromRow(inst) {
+    return {
+        ...(typeof inst.start_date === 'string' ? { startedAt: inst.start_date } : {}),
+        ...(typeof inst.end_date === 'string' ? { finishedAt: inst.end_date } : {}),
+        ...(typeof inst.size === 'number' ? { outputBytes: inst.size } : {}),
+    };
+}
 async function feedInstances_load(feedID) {
     const cache = (0, cumin_1.procCache_get)();
     const client = await cumin_1.chrisConnection.client_get();
@@ -117,6 +127,7 @@ async function feedInstances_load(feedID) {
             params: null,
             outputPath: outputPath_normalize(inst.output_path) ?? undefined,
             status: String(inst.status ?? 'unknown'),
+            ...instanceMetrics_fromRow(inst),
         });
     }
     cache.topologyLoaded_mark(feedID);
@@ -169,11 +180,26 @@ function procPath_parse(pathStr) {
     let feedID = null;
     let instanceID = null;
     let virtualFile = null;
+    let dataRemainder = null;
     if (parts.length >= 1) {
         const feedMatch = parts[0].match(/^feed_(\d+)$/);
         if (feedMatch)
             feedID = parseInt(feedMatch[1], 10);
     }
+    // A `data` segment directly after an instance segment starts the link's
+    // subtree: the instance is the one before it, whatever follows is the
+    // remainder inside the CFS target.
+    for (let index = 2; index < parts.length; index++) {
+        if (parts[index] !== 'data')
+            continue;
+        const instMatch = parts[index - 1].match(/_(\d+)$/);
+        if (!instMatch)
+            continue;
+        instanceID = parseInt(instMatch[1], 10);
+        virtualFile = 'data';
+        dataRemainder = parts.slice(index + 1).join('/');
+        return { feedID, instanceID, virtualFile, dataRemainder };
+    }
     if (parts.length >= 2) {
         const lastPart = parts[parts.length - 1];
         if (FEED_FILES.has(lastPart) || INSTANCE_FILES.has(lastPart)) {
@@ -190,7 +216,7 @@ function procPath_parse(pathStr) {
                 instanceID = parseInt(instMatch[1], 10);
         }
     }
-    return { feedID, instanceID, virtualFile };
+    return { feedID, instanceID, virtualFile, dataRemainder };
 }
 /** Formats instance params as key=value lines. */
 function params_render(inst) {
@@ -218,6 +244,21 @@ function outputPath_normalize(value) {
  * @param instanceID - Plugin-instance ID whose output path is needed.
  * @returns Absolute output path, or null when CUBE has not recorded one.
  */
+/**
+ * Resolves a path inside an instance's `data` link to its CFS target.
+ *
+ * @param instanceID - The instance whose output space the path enters.
+ * @param remainder - The path below `data`, '' for the link itself.
+ * @returns The absolute CFS path, or Err when the job has no output space.
+ */
+async function dataTarget_resolve(instanceID, remainder) {
+    const outputPath = await instanceOutputPath_ensure(instanceID);
+    if (!outputPath) {
+        cumin_1.errorStack.stack_push('error', `No CFS output path is available for job ${instanceID}`);
+        return (0, cumin_1.Err)();
+    }
+    return (0, cumin_1.Ok)(remainder === '' ? outputPath : `${outputPath}/${remainder}`);
+}
 async function instanceOutputPath_ensure(instanceID) {
     const cache = (0, cumin_1.procCache_get)();
     const inst = cache.instance_get(instanceID);
@@ -317,7 +358,17 @@ class ProcVfsProvider {
             });
             return (0, cumin_1.Ok)(items);
         }
-        const { feedID, instanceID } = procPath_parse(clean);
+        const { feedID, instanceID, virtualFile, dataRemainder } = procPath_parse(clean);
+        // Anything under an instance's `data` link belongs to the link's CFS
+        // target: resolve and delegate, so `ls .../data` (and deeper) shows the
+        // target's real contents instead of silently re-listing the instance.
+        if (instanceID !== null && virtualFile === 'data' && dataRemainder !== null) {
+            const target = await dataTarget_resolve(instanceID, dataRemainder);
+            if (!target.ok)
+                return (0, cumin_1.Err)();
+            const { vfsDispatcher } = await import('../dispatcher.js');
+            return vfsDispatcher.list(target.value, _options);
+        }
         // /proc/jobs/feed_N — list root instances + feed virtual files
         if (feedID !== null && instanceID === null) {
             const wasLoaded = cache.topologyLoaded_has(feedID);
@@ -391,11 +442,40 @@ class ProcVfsProvider {
         }
         return (0, cumin_1.Ok)([]);
     }
+    /**
+     * Binary bytes exist only under the `data` link (an image in a job's
+     * output space); everything else in `/proc` is synthesized text.
+     *
+     * @param pathStr - Absolute `/proc/jobs/.../data/...` path.
+     * @returns The target file's bytes.
+     */
+    async readBinary(pathStr) {
+        await cache_ensure();
+        const clean = pathStr.replace(/\/$/, '');
+        const { instanceID, virtualFile, dataRemainder } = procPath_parse(clean);
+        if (instanceID === null || virtualFile !== 'data' || dataRemainder === null || dataRemainder === '') {
+            cumin_1.errorStack.stack_push('error', `${pathStr} is not a binary file.`);
+            return (0, cumin_1.Err)();
+        }
+        const target = await dataTarget_resolve(instanceID, dataRemainder);
+        if (!target.ok)
+            return (0, cumin_1.Err)();
+        const { vfsDispatcher } = await import('../dispatcher.js');
+        return vfsDispatcher.readBinary(target.value);
+    }
     async read(pathStr) {
         await cache_ensure();
         const cache = (0, cumin_1.procCache_get)();
         const clean = pathStr.replace(/\/$/, '');
-        const { feedID, instanceID, virtualFile } = procPath_parse(clean);
+        const { feedID, instanceID, virtualFile, dataRemainder } = procPath_parse(clean);
+        // A file under the `data` link is the CFS target's file.
+        if (instanceID !== null && virtualFile === 'data' && dataRemainder !== null && dataRemainder !== '') {
+            const target = await dataTarget_resolve(instanceID, dataRemainder);
+            if (!target.ok)
+                return (0, cumin_1.Err)();
+            const { vfsDispatcher } = await import('../dispatcher.js');
+            return vfsDispatcher.read(target.value);
+        }
         // Feed-level virtual files
         if (feedID !== null && instanceID === null && virtualFile !== null) {
             const feed = cache.feed_get(feedID);
@@ -556,6 +636,7 @@ async function feedStatus_refresh(feedID) {
     for await (const step of (0, cumin_1.listPages_walk)((offset, limit) => (0, cumin_1.pluginInstancesPage_get)(client, { feed_id: feedID, limit, offset }), { pageSize: PAGE })) {
         for (const inst of step.items) {
             cache.status_update(Number(inst.id), String(inst.status ?? 'unknown'));
+            cache.instanceMetrics_set(Number(inst.id), instanceMetrics_fromRow(inst));
         }
     }
 }
@@ -606,6 +687,7 @@ async function procTopology_run(state) {
                 params: null,
                 outputPath: outputPath_normalize(inst.output_path) ?? undefined,
                 status: String(inst.status ?? 'unknown'),
+                ...instanceMetrics_fromRow(inst),
             });
             state.seenInstanceIDs.add(instanceID);
             state.seenFeedIDs.add(feedID);
@@ -655,6 +737,7 @@ function procTopology_start(state) {
         if ((0, cumin_1.procCache_get)().warmupComplete) {
             procTopologyFailure = undefined;
             procTopologyResumeState = null;
+            procSettlementTails_run();
         }
         else {
             procTopologyFailure = 'the topology sweep ended before the index completed';
@@ -668,6 +751,17 @@ function procTopology_start(state) {
     });
     return sweep;
 }
+/**
+ * Kicks the quiet settlement tails once the topology index is complete:
+ * every unresolved `ts` join resolves in the background (so first diagrams
+ * are pure cache, and the checkpoint persists them), and the pipeline
+ * package store sweeps unseen registered pipelines. Both are best-effort —
+ * a failure leaves the lazy paths intact.
+ */
+function procSettlementTails_run() {
+    void (0, feedJoins_js_1.procJoins_sweep)().catch(() => { });
+    void (0, packages_js_1.pipelinePackages_sweep)().catch(() => { });
+}
 /**
  * Runs a feed-scoped topology reconciliation selected after checkpoint restore.
  *
@@ -680,6 +774,7 @@ async function procTopologyScoped_run(feedIDs) {
     for (const feedID of feedIDs)
         await procCache_refresh(feedID);
     cache.warmup_complete();
+    procSettlementTails_run();
 }
 /**
  * Starts one scoped reconciliation and retains its targets for `proc retry`.