@fnndsc/salsa 3.5.1 → 3.6.1

package/dist/vfs/providers/pacs.js

@@ -12,6 +12,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PacsVfsProvider = void 0;
 const cumin_1 = require("@fnndsc/cumin");
+const watch_js_1 = require("../../retrieve/watch.js");
 const sort_js_1 = require("../sort.js");
 const pacsHelpers_js_1 = require("./pacsHelpers.js");
 const index_js_1 = require("../../pacs/index.js");
@@ -19,28 +20,6 @@ const index_js_2 = require("../../files/index.js");
 const path_1 = __importDefault(require("path"));
 const chalk_1 = __importDefault(require("chalk"));
 const pacs_content_js_1 = require("./pacs_content.js");
-/**
- * Resolves the folder path on ChRIS storage for a retrieved series.
- *
- * @param seriesInstanceUID - The Series Instance UID to resolve.
- * @returns Promise resolving to the folder path string or null on failure.
- */
-async function series_getFolderPath(seriesInstanceUID) {
-    const client = await cumin_1.chrisConnection.client_get();
-    if (!client) {
-        return null;
-    }
-    const seriesList = await client.getPACSSeriesList({
-        SeriesInstanceUID: seriesInstanceUID,
-        limit: 1,
-    });
-    const seriesItems = seriesList.getItems();
-    if (!seriesItems || seriesItems.length === 0) {
-        return null;
-    }
-    const series = seriesItems[0];
-    return series?.data?.folder_path || null;
-}
 function pacsRoot_list() {
     return (0, cumin_1.Ok)([{ name: "queries", type: "vfs", size: 0, owner: "root", date: new Date().toISOString() }]);
 }
@@ -126,16 +105,17 @@ function seriesToRetrieve_build(decoded, studyUID, seriesUID, src) {
     }
     const seriesArray = (0, pacsHelpers_js_1.series_extractFromStudy)(studyObj);
     const seriesToRetrieve = [];
+    const expected_of = (obj) => Number((0, pacsHelpers_js_1.tag_extractValue)(obj?.NumberOfSeriesRelatedInstances ?? 0)) || 0;
     if (seriesUID) {
         const seriesObj = (0, pacsHelpers_js_1.series_findByUID)(seriesArray, seriesUID);
         const desc = seriesObj ? (0, pacsHelpers_js_1.tag_extractValue)(seriesObj.SeriesDescription || "Series") : "Series";
-        seriesToRetrieve.push({ uid: seriesUID, description: desc });
+        seriesToRetrieve.push({ uid: seriesUID, description: desc, expectedFiles: expected_of(seriesObj) });
     }
     else {
         for (const s of seriesArray) {
             const sUID = (0, pacsHelpers_js_1.tag_extractValue)(s.SeriesInstanceUID || s.uid);
             if (sUID) {
-                seriesToRetrieve.push({ uid: sUID, description: (0, pacsHelpers_js_1.tag_extractValue)(s.SeriesDescription || "Series") });
+                seriesToRetrieve.push({ uid: sUID, description: (0, pacsHelpers_js_1.tag_extractValue)(s.SeriesDescription || "Series"), expectedFiles: expected_of(s) });
             }
         }
     }
@@ -156,98 +136,69 @@ async function pacsServer_resolve() {
     cumin_1.errorStack.stack_push("error", "cp: No PACS server available or configured in context.");
     return (0, cumin_1.Err)();
 }
-async function retrieve_pollUntilComplete(syntheticQueryId, seriesUID, maxAttempts) {
-    let attempts = 0;
-    while (attempts < maxAttempts) {
-        attempts++;
-        await new Promise((resolve) => setTimeout(resolve, 5000));
-        const statusResult = await (0, index_js_1.pacsRetrieve_statusForQuery)(syntheticQueryId);
-        if (!statusResult.ok || !statusResult.value) {
-            console.log(chalk_1.default.yellow(`     [Attempt ${attempts}/${maxAttempts}] Failed to fetch status report, retrying...`));
-            continue;
-        }
-        const statusReport = statusResult.value;
-        let totalExpected = 0;
-        let totalActual = 0;
-        let anyPulling = false;
-        let allPulled = true;
-        let anyError = false;
-        if (statusReport.studies) {
-            for (const s of statusReport.studies) {
-                if (s.series) {
-                    for (const ser of s.series) {
-                        if (String(ser.seriesInstanceUID) === String(seriesUID)) {
-                            totalExpected = Number(ser.expectedFiles) || 0;
-                            totalActual = Number(ser.actualFiles) || 0;
-                            if (ser.status === "pulling")
-                                anyPulling = true;
-                            if (ser.status !== "pulled")
-                                allPulled = false;
-                            if (ser.status === "error")
-                                anyError = true;
-                        }
-                    }
+async function series_retrieveAndCopy(seriesItem, studyUID, pacsserver, dest, idx, total) {
+    (0, cumin_1.runtimeOutput_data)(`${chalk_1.default.cyan(`\n[PACS Retrieve ${idx + 1}/${total}] Processing series: ${seriesItem.description} (${seriesItem.uid})...`)}\n`);
+    const client = await cumin_1.chrisConnection.client_get();
+    if (!client) {
+        (0, cumin_1.runtimeOutput_err)(`${chalk_1.default.red("  ✗ Not connected to ChRIS.")}\n`);
+        return false;
+    }
+    // One retrieve engine for cp and pull alike: bounded, retried firing plus
+    // the LONK watch, replacing this provider's former 5-second polling loop.
+    const task = (0, watch_js_1.retrieveTask_make)({
+        label: seriesItem.description,
+        seriesUID: seriesItem.uid,
+        studyUID,
+        pacsName: pacsserver,
+        // The decode's instance count enables the idempotency skip: a series
+        // already fully registered in CUBE is copied without refiring.
+        expectedFiles: seriesItem.expectedFiles,
+    });
+    const alreadyThere = await (0, watch_js_1.retrieveTasks_skipComplete)([task]);
+    if (alreadyThere === 0) {
+        const events = {
+            task: (t, status) => {
+                if (status === 'running' && t.actualFiles > 0) {
+                    (0, cumin_1.runtimeOutput_data)(`${chalk_1.default.gray(`     ${t.actualFiles} file(s) received...`)}\n`);
                 }
-            }
-        }
-        const overallStatus = statusReport.retrieveStatus || "pending";
-        console.log(chalk_1.default.gray(`     [Attempt ${attempts}/${maxAttempts}] CUBE Status: ${overallStatus} | Files: ${totalActual}/${totalExpected}`));
-        if (allPulled && totalExpected > 0 && totalActual === totalExpected) {
-            console.log(chalk_1.default.green(`  ✓ Pull complete: ${totalActual}/${totalExpected} files retrieved.`));
-            return true;
-        }
-        if (overallStatus === "succeeded" || overallStatus === "completed") {
-            console.log(chalk_1.default.green(`  ✓ Pull complete (Status: ${overallStatus}).`));
-            return true;
+                else if (status === 'error') {
+                    (0, cumin_1.runtimeOutput_err)(`${chalk_1.default.red("  ✗ PACS retrieve reported an error.")}\n`);
+                }
+                else if (status === 'stalled' || status === 'timeout') {
+                    (0, cumin_1.runtimeOutput_err)(`${chalk_1.default.red(`  ✗ PACS retrieve ${status}.`)}\n`);
+                }
+            },
+        };
+        (0, cumin_1.runtimeOutput_data)(`${chalk_1.default.gray("  -> Firing PACS retrieve and watching progress...")}\n`);
+        const firingErrors = await (0, watch_js_1.retrieve_fireAndWatch)([task], pacsserver, client, events);
+        if (firingErrors > 0) {
+            (0, cumin_1.runtimeOutput_err)(`${chalk_1.default.red(`  ✗ Retrieve could not be fired for series ${seriesItem.uid}.`)}\n`);
+            return false;
         }
-        if (anyError || overallStatus === "error" || overallStatus === "failed") {
-            console.error(chalk_1.default.red("  ✗ PACS retrieve reported error status."));
+        if (task.status !== 'pulled') {
             return false;
         }
     }
-    console.error(chalk_1.default.red("  ✗ PACS retrieve timed out."));
-    return false;
-}
-async function series_retrieveAndCopy(seriesItem, studyUID, pacsserver, dest, idx, total) {
-    console.log(chalk_1.default.cyan(`\n[PACS Retrieve ${idx + 1}/${total}] Processing series: ${seriesItem.description} (${seriesItem.uid})...`));
-    const queryPayload = {
-        title: `Synthetic cp Query ${seriesItem.uid}`,
-        query: JSON.stringify({ SeriesInstanceUID: seriesItem.uid, StudyInstanceUID: studyUID }),
-        execute: false,
-    };
-    console.log(chalk_1.default.gray("  -> Registering synthetic query on CUBE..."));
-    const queryResult = await (0, index_js_1.pacsQueries_create)(pacsserver, queryPayload);
-    if (!queryResult.ok) {
-        console.error(chalk_1.default.red(`  ✗ Failed to create synthetic query for series ${seriesItem.uid}`));
-        return false;
-    }
-    const syntheticQueryId = queryResult.value.id;
-    console.log(chalk_1.default.gray(`  -> Triggering PACS retrieve (Query ID: ${syntheticQueryId})...`));
-    const retrieveResult = await (0, index_js_1.pacsRetrieve_create)(syntheticQueryId);
-    if (!retrieveResult.ok) {
-        console.error(chalk_1.default.red(`  ✗ Failed to create PACS retrieve for query ${syntheticQueryId}`));
-        return false;
+    (0, cumin_1.runtimeOutput_data)(`${chalk_1.default.gray("  -> Finding folder path on ChRIS storage...")}\n`);
+    let folderPath = task.cubePathDir;
+    if (folderPath === null) {
+        const stateResult = await (0, cumin_1.seriesStorage_resolve)(seriesItem.uid, { attempts: 4, delayMs: 2_000 });
+        folderPath = stateResult.ok ? stateResult.value.folderPath : null;
     }
-    console.log(chalk_1.default.gray("  -> Pulling series data sequentially, polling progress..."));
-    const finished = await retrieve_pollUntilComplete(syntheticQueryId, seriesItem.uid, 60);
-    if (!finished)
-        return false;
-    console.log(chalk_1.default.gray("  -> Finding folder path on ChRIS storage..."));
-    const folderPath = await series_getFolderPath(seriesItem.uid);
     if (!folderPath) {
-        console.error(chalk_1.default.red(`  ✗ No registered folder path found for series UID ${seriesItem.uid}`));
+        (0, cumin_1.runtimeOutput_err)(`${chalk_1.default.red(`  ✗ No registered folder path found for series UID ${seriesItem.uid}`)}\n`);
         return false;
     }
     const absoluteFolderPath = folderPath.startsWith("/") ? folderPath : "/" + folderPath;
     const cleanDesc = seriesItem.description.replace(/[\s/]/g, "_");
     const targetSeriesFolder = path_1.default.posix.join(dest, `Series_${seriesItem.uid}_${cleanDesc}`);
-    console.log(chalk_1.default.gray(`  -> Copying series files to '${targetSeriesFolder}'...`));
+    (0, cumin_1.runtimeOutput_data)(`${chalk_1.default.gray(`  -> Copying series files to '${targetSeriesFolder}'...`)}\n`);
     const copySuccess = await (0, index_js_2.files_copyRecursively)(absoluteFolderPath, targetSeriesFolder);
     if (!copySuccess) {
-        console.error(chalk_1.default.red(`  ✗ Recursive copy failed from '${absoluteFolderPath}' to '${targetSeriesFolder}'`));
+        (0, cumin_1.runtimeOutput_err)(`${chalk_1.default.red(`  ✗ Recursive copy failed from '${absoluteFolderPath}' to '${targetSeriesFolder}'`)}\n`);
         return false;
     }
-    console.log(chalk_1.default.green(`  ✓ Series '${seriesItem.description}' copied successfully.`));
+    (0, cumin_1.runtimeOutput_data)(`${chalk_1.default.green(`  ✓ Series '${seriesItem.description}' copied successfully.`)}\n`);
     return true;
 }
 /**
@@ -256,8 +207,20 @@ async function series_retrieveAndCopy(seriesItem, studyUID, pacsserver, dest, id
 class PacsVfsProvider {
     /** Prefix matches /net/pacs and subdirectories. */
     prefix = "/net/pacs";
-    /** Cache for decoded PACS query results to avoid redundant API hits. */
+    /**
+     * Cache for decoded PACS query results to avoid redundant API hits.
+     *
+     * Contract (see docs/code-audit-2026-08.adoc, cache inventory): only a
+     * settled result — one carrying a structured `json` payload — is cached,
+     * since a query's payload is written once and never mutates afterwards; a
+     * payload-less decode (query still running, or empty) is re-fetched on the
+     * next access. The cache is size-bounded so a long-lived daemon does not
+     * grow it monotonically; eviction is oldest-inserted-first, which for
+     * monotonically increasing query ids approximates least-recently-created.
+     */
     _queryCache = new Map();
+    /** Upper bound on cached decoded query results. */
+    static QUERY_CACHE_MAX = 100;
     /**
      * Fetches the decoded query result, leveraging a cache to prevent redundant API calls.
      *
@@ -273,7 +236,17 @@ class PacsVfsProvider {
         if (!decodedResult.ok || !decodedResult.value) {
             return null;
         }
-        this._queryCache.set(queryId, decodedResult.value);
+        // Cache settled results only: a decode without a structured payload may
+        // be a still-running query whose payload arrives later, and caching it
+        // would pin the empty view for the life of the process.
+        if (decodedResult.value.json !== undefined && decodedResult.value.json !== null) {
+            if (this._queryCache.size >= PacsVfsProvider.QUERY_CACHE_MAX) {
+                const oldest = this._queryCache.keys().next().value;
+                if (oldest !== undefined)
+                    this._queryCache.delete(oldest);
+            }
+            this._queryCache.set(queryId, decodedResult.value);
+        }
         return decodedResult.value;
     }
     /**
@@ -309,16 +282,22 @@ class PacsVfsProvider {
                 return studies_list(studies, options);
             const studyUID = parts[4].replace(/^Study_/, "").split("_")[0];
             const studyObj = (0, pacsHelpers_js_1.study_findByUID)(studies, studyUID);
-            if (!studyObj)
-                return (0, cumin_1.Ok)([]);
+            // A missing UID is "no such directory", never an empty one: rendering
+            // not-found as an empty listing hides typos and stale paths entirely.
+            if (!studyObj) {
+                cumin_1.errorStack.stack_push("error", `'${effectivePath}': No such study in query ${queryId}. Use 'ls' on the query directory to see available studies.`);
+                return (0, cumin_1.Err)();
+            }
             const seriesArr = (0, pacsHelpers_js_1.series_extractFromStudy)(studyObj);
             if (parts.length === 5)
                 return series_list(seriesArr, options);
             if (parts.length === 6) {
                 const seriesUID = parts[5].replace(/^Series_/, "").split("_")[0];
                 const seriesObj = (0, pacsHelpers_js_1.series_findByUID)(seriesArr, seriesUID);
-                if (!seriesObj)
-                    return (0, cumin_1.Ok)([]);
+                if (!seriesObj) {
+                    cumin_1.errorStack.stack_push("error", `'${effectivePath}': No such series in study ${studyUID}.`);
+                    return (0, cumin_1.Err)();
+                }
                 return seriesFiles_list(seriesObj);
             }
             return (0, cumin_1.Ok)([]);
@@ -355,7 +334,7 @@ class PacsVfsProvider {
             if (!serverResult.ok)
                 return false;
             const pacsserver = serverResult.value;
-            console.log(chalk_1.default.cyan(`[PACS Retrieve] Initiating sequential gather of ${seriesToRetrieve.length} series...`));
+            (0, cumin_1.runtimeOutput_data)(`${chalk_1.default.cyan(`[PACS Retrieve] Initiating sequential gather of ${seriesToRetrieve.length} series...`)}\n`);
             let overallSuccess = true;
             for (let i = 0; i < seriesToRetrieve.length; i++) {
                 const ok = await series_retrieveAndCopy(seriesToRetrieve[i], studyUID, pacsserver, dest, i, seriesToRetrieve.length);

package/dist/vfs/providers/pacs.js.map

@@ -1 +1 @@
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package/dist/vfs/providers/pacsHelpers.js

@@ -84,21 +84,25 @@ function series_findByUID(seriesArr, uid) {
 function cpSrc_parse(src) {
     const absolutePath = src.startsWith("/") ? src : "/" + src;
     const parts = absolutePath.split("/").filter(Boolean);
-    if (parts.length < 4) {
+    // Locate the query folder by its `_qid:` marker rather than by position:
+    // real listing paths are /net/pacs/queries/<qfolder>/Study_/Series_, and a
+    // fixed-offset parse silently rejected every one of them.
+    const queryIdx = parts.findIndex((part) => /_qid:\d+/.test(part));
+    if (queryIdx === -1 || parts.length < queryIdx + 2) {
         cumin_1.errorStack.stack_push("error", `cp: Copying from '${src}' is not supported. Please specify a Study or Series directory.`);
         return (0, cumin_1.Err)();
     }
-    const studyFolder = parts[3];
+    const studyFolder = parts[queryIdx + 1];
     if (!studyFolder.startsWith("Study_")) {
         cumin_1.errorStack.stack_push("error", `cp: Invalid PACS Study folder format: '${studyFolder}'`);
         return (0, cumin_1.Err)();
     }
     const studyUID = studyFolder.replace(/^Study_/, "").split("_")[0];
     let seriesUID;
-    if (parts.length >= 5 && parts[4].startsWith("Series_")) {
-        seriesUID = parts[4].replace(/^Series_/, "").split("_")[0];
+    if (parts.length >= queryIdx + 3 && parts[queryIdx + 2].startsWith("Series_")) {
+        seriesUID = parts[queryIdx + 2].replace(/^Series_/, "").split("_")[0];
     }
-    const queryId = queryId_extractFromFolder(parts[2]);
+    const queryId = queryId_extractFromFolder(parts[queryIdx]);
     if (Number.isNaN(queryId)) {
         cumin_1.errorStack.stack_push("error", `cp: Invalid query ID in path '${src}'`);
         return (0, cumin_1.Err)();

package/dist/vfs/providers/pacsHelpers.js.map

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

@@ -43,6 +43,15 @@ export declare function procPath_parse(pathStr: string): {
  */
 export declare class ProcVfsProvider implements VFSProvider {
     readonly prefix: string;
+    /**
+     * Resolves the synthetic `data` link for one job only when navigation asks
+     * to follow it. This keeps `/proc` topology listings and recursive trees
+     * entirely cache-backed.
+     *
+     * @param pathStr - Absolute `/proc/jobs/.../data` path to resolve.
+     * @returns The authoritative CFS output path, or an error when absent.
+     */
+    linkTarget_resolve(pathStr: string): Promise<Result<string>>;
     list(pathStr: string, _options?: {
         sort?: 'name' | 'size' | 'date' | 'owner';
         reverse?: boolean;
@@ -90,6 +99,23 @@ export declare function feedStatus_refresh(feedID: number): Promise<void>;
  * @returns The single in-flight sweep promise.
  */
 export declare function procTopology_warmup(): Promise<void>;
+/**
+ * Reconciles topology only for feed IDs selected by a restored-cache feed-index
+ * comparison. This preserves the checkpointed topology for unchanged terminal
+ * feeds while refreshing new, changed, and active feeds from CUBE.
+ *
+ * @param feedIDs - Canonical CUBE feed IDs whose topology must be reloaded.
+ * @returns A promise that resolves after all supplied feeds have been refreshed.
+ */
+export declare function procTopology_reconcileFeeds(feedIDs: number[]): Promise<void>;
+/**
+ * Continues a failed topology reconciliation from its retained global page or
+ * scoped feed set.
+ *
+ * @returns The resumed sweep promise, or the active sweep when one is running.
+ * @throws {Error} When there is no failed sweep continuation to retry.
+ */
+export declare function procTopology_retry(): Promise<void>;
 /**
  * Reports the session topology sweep lifecycle.
  *
@@ -105,5 +131,12 @@ export declare function procTopology_status(): ProcTopologyStatus;
 export declare function procTopology_await(): Promise<void>;
 /**
  * Rebuilds the ProcCache, optionally scoped to one feed.
+ *
+ * A full refresh returns feeds whose topology merits reload after the feed-index
+ * comparison. Callers performing an explicit `proc refresh` can ignore that
+ * result and run a global topology sweep; restored startup uses it to stay scoped.
+ *
+ * @param feedID - One feed to force-refresh, or undefined for the full feed index.
+ * @returns IDs whose topology is new, changed, or currently active.
  */
-export declare function procCache_refresh(feedID?: number): Promise<void>;
+export declare function procCache_refresh(feedID?: number): Promise<number[]>;