@fnndsc/cumin 3.17.0 → 3.18.0

package/dist/io/chrisIO.js

@@ -290,17 +290,30 @@ class ChrisIO {
             const timeoutPromise = new Promise((_, reject) => setTimeout(() => reject(new Error('Upload timeout after 30s')), 30000));
             const userFile = await Promise.race([uploadPromise, timeoutPromise]);
             // ChRIS may rename the file to avoid collisions (e.g. world.txt → world_XXXXXXX.txt)
-            // when the path was recently deleted and not yet committed. Detect and rename back.
+            // when the path was recently deleted and not yet committed. Renaming
+            // it back is right THEN and catastrophic when the path is genuinely
+            // occupied: a write onto a path the store already holds leaves a row
+            // CUBE's own API cannot serve, and one such row makes every listing
+            // of that folder fail (docs/CUBE-gaps.adoc). So the rename happens
+            // only when the wanted path is free, and a check that cannot answer
+            // counts as occupied — the safe reading, since the cost of guessing
+            // wrong is the operator's folder.
             const actualFname = (0, adapter_js_1.itemData_get)(userFile)?.fname ?? '';
             const normalizedActual = actualFname.startsWith('/') ? actualFname.substring(1) : actualFname;
             if (normalizedActual && normalizedActual !== fullPath) {
-                try {
-                    await userFile.put({ upload_path: fullPath });
+                const free = await this.path_isFree(client, fullPath, normalizedActual);
+                if (!free) {
+                    errorStack_js_1.errorStack.stack_push('warning', `'${fullPath}' already exists — the upload landed as '${actualFname}' rather than overwriting it`);
                 }
-                catch (renameErr) {
-                    const renameMsg = renameErr instanceof Error ? renameErr.message : String(renameErr);
-                    errorStack_js_1.errorStack.stack_push('warning', `Uploaded as '${actualFname}' — rename to '${fullPath}' failed: ${renameMsg}`);
-                    // Don't fail the upload — file was uploaded, just at wrong name
+                else {
+                    try {
+                        await userFile.put({ upload_path: fullPath });
+                    }
+                    catch (renameErr) {
+                        const renameMsg = renameErr instanceof Error ? renameErr.message : String(renameErr);
+                        errorStack_js_1.errorStack.stack_push('warning', `Uploaded as '${actualFname}' — rename to '${fullPath}' failed: ${renameMsg}`);
+                        // Don't fail the upload — file was uploaded, just at wrong name
+                    }
                 }
             }
             return true;
@@ -311,6 +324,69 @@ class ChrisIO {
             return false;
         }
     }
+    /**
+     * Deletes one file by its id, without listing anything.
+     *
+     * A file that cannot be LISTED must still be deletable: a folder whose
+     * listing the server refuses is exactly the folder an operator most needs
+     * to clear, and a delete that resolves its id through the parent's
+     * collection cannot help there (#462).
+     *
+     * @param fileId - The file's id.
+     * @returns Ok(true) when the file is gone, Err when the server refused.
+     */
+    async file_deleteById(fileId) {
+        const client = await this.client_get();
+        if (!client) {
+            errorStack_js_1.errorStack.stack_push("error", "ChRIS client is not initialized");
+            return (0, result_js_1.Err)();
+        }
+        try {
+            const userFile = await client.getUserFile(fileId);
+            if (!userFile) {
+                errorStack_js_1.errorStack.stack_push("error", `File not found with ID ${fileId}`);
+                return (0, result_js_1.Err)();
+            }
+            await (0, adapter_js_1.resource_call)(userFile, '_delete');
+            return (0, result_js_1.Ok)(true);
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push("error", `Failed to delete file ID ${fileId}: ${message}`);
+            return (0, result_js_1.Err)();
+        }
+    }
+    /**
+     * Whether a path is free to be written to.
+     *
+     * Asked by exact name rather than by listing the folder: one request, and
+     * it still answers when the folder's own listing is broken. Anything the
+     * server will not answer counts as occupied.
+     *
+     * @param client - The connected client.
+     * @param wanted - The path a write wants, without a leading slash.
+     * @param mine - The path the just-uploaded file currently occupies, which
+     *   is not a collision with itself.
+     * @returns True when nothing else holds the path.
+     */
+    async path_isFree(client, wanted, mine) {
+        try {
+            // listing-bound: one exact path can only be held by one file; five is
+            // room for a server that answers loosely, not a page of a collection.
+            const held = await client.getUserFiles({ limit: 5, fname_exact: wanted });
+            const items = held.getItems() ?? [];
+            for (const item of items) {
+                const fname = (0, adapter_js_1.itemData_get)(item)?.fname ?? '';
+                const normalized = fname.startsWith('/') ? fname.substring(1) : fname;
+                if (normalized !== mine)
+                    return false;
+            }
+            return true;
+        }
+        catch {
+            return false;
+        }
+    }
     /**
      * Creates a new folder in ChRIS at the specified path.
      *

package/dist/io/chrisIO.js.map

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package/dist/pacs/chrisPACS.d.ts

@@ -50,6 +50,14 @@ export interface PACSQueryRecord {
 export interface PACSQueryListOptions extends ListOptions {
     pacs_id?: number;
     pacs_identifier?: string;
+    /** Records created at or after this ISO timestamp. */
+    min_creation_date?: string;
+    /** Records created at or before this ISO timestamp. */
+    max_creation_date?: string;
+    /** Records owned by this username. */
+    owner_username?: string;
+    /** Records in this state, e.g. `succeeded`. */
+    status?: string;
 }
 /**
  * Group handler for PACS queries.

package/dist/pacs/chrisPACS.js.map

@@ -1 +1 @@
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package/dist/pacs/queryIndexSweep.d.ts

@@ -0,0 +1,69 @@
+import { Result } from "../utils/result.js";
+import { type QueryIndexEntry } from "../cache/queryIndex.js";
+import { type PACSQueryListOptions } from "./chrisPACS.js";
+/**
+ * How many records a sweep asks for at a time.
+ *
+ * Not a cap on what is indexed — the sweep pages until the collection is
+ * exhausted. Every row carries its compressed result whether or not this
+ * wants it, so the page is kept modest to bound each request rather than
+ * the walk.
+ */
+export declare const QUERY_SWEEP_PAGE: number;
+/**
+ * A safety stop on the number of pages one sweep will walk.
+ *
+ * The walk is bounded by the collection, not by this; the bound exists so
+ * that a CUBE which never reports a short page cannot spin forever behind
+ * the prompt. Reaching it is reported, never silent — a truncated index
+ * that says nothing is the defect this whole slice exists to remove.
+ */
+export declare const QUERY_SWEEP_PAGE_MAX: number;
+/**
+ * The listing the index feeds.
+ *
+ * A sweep that learns of queries the cached listing never had must drop
+ * that listing, or the operator keeps seeing the old truncated one until
+ * its TTL happens to expire — which is the same invisible-tail defect from
+ * a different direction.
+ */
+export declare const QUERY_LOG_PATH: string;
+/** What a sweep did, for the boot readout that reports it. */
+export interface QuerySweepResult {
+    /** Records newly filed. */
+    indexed: number;
+    /** True when the sweep resumed from a restored index rather than rebuilding. */
+    resumed: boolean;
+    /** Pages fetched. */
+    pages: number;
+    /** True when the page bound stopped the walk before the collection did. */
+    bounded: boolean;
+}
+/**
+ * Turns one CUBE query record into an index entry.
+ *
+ * @param row - A row of the `pacs/queries` collection.
+ * @returns The entry, or null when the row carries no usable criteria.
+ */
+export declare function queryRow_toEntry(row: Record<string, unknown>): QueryIndexEntry | null;
+/**
+ * Files one query record, so the next identical question finds it.
+ *
+ * Called on every query mise runs. The index is then correct for anything
+ * this session did without the sweep having reached that far.
+ *
+ * @param row - The query record as CUBE returned it.
+ */
+export declare function queryIndex_note(row: Record<string, unknown>): void;
+/**
+ * Walks the query collection into the index.
+ *
+ * Newest first, resuming from the index's floor, until the collection is
+ * exhausted. Filters server-side by owner and status where those are given,
+ * since a query someone else asked, or one that failed, can never answer
+ * this identity's question.
+ *
+ * @param options - Server-side narrowing, typically owner and status.
+ * @returns What the sweep filed, or Err with the reason on the stack.
+ */
+export declare function queryIndex_sweep(options?: PACSQueryListOptions): Promise<Result<QuerySweepResult>>;

package/dist/pacs/queryIndexSweep.js

@@ -0,0 +1,159 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.QUERY_LOG_PATH = exports.QUERY_SWEEP_PAGE_MAX = exports.QUERY_SWEEP_PAGE = void 0;
+exports.queryRow_toEntry = queryRow_toEntry;
+exports.queryIndex_note = queryIndex_note;
+exports.queryIndex_sweep = queryIndex_sweep;
+/**
+ * @file Filling the PACS query index from CUBE.
+ *
+ * CUBE cannot be asked which stored query had given criteria, so the
+ * collection is walked and what it holds is remembered. Two ways in:
+ *
+ * - `queryIndex_note` files one record, called whenever mise runs a query,
+ *   so the common case never waits for a sweep at all;
+ * - `queryIndex_sweep` walks the back catalogue behind the prompt, newest
+ *   first, resuming from the index's floor so it never re-walks what it
+ *   already holds.
+ *
+ * The sweep is deliberately a background step. Every row of every page
+ * drags its compressed result along, so this is the expensive path — worth
+ * paying once, off the boot gate, never in front of an operator's query.
+ *
+ * @module
+ */
+const errorStack_js_1 = require("../error/errorStack.js");
+const result_js_1 = require("../utils/result.js");
+const queryIndex_js_1 = require("../cache/queryIndex.js");
+const chrisPACS_js_1 = require("./chrisPACS.js");
+const listCache_js_1 = require("../cache/listCache.js");
+/**
+ * How many records a sweep asks for at a time.
+ *
+ * Not a cap on what is indexed — the sweep pages until the collection is
+ * exhausted. Every row carries its compressed result whether or not this
+ * wants it, so the page is kept modest to bound each request rather than
+ * the walk.
+ */
+exports.QUERY_SWEEP_PAGE = 100;
+/**
+ * A safety stop on the number of pages one sweep will walk.
+ *
+ * The walk is bounded by the collection, not by this; the bound exists so
+ * that a CUBE which never reports a short page cannot spin forever behind
+ * the prompt. Reaching it is reported, never silent — a truncated index
+ * that says nothing is the defect this whole slice exists to remove.
+ */
+exports.QUERY_SWEEP_PAGE_MAX = 200;
+/**
+ * The listing the index feeds.
+ *
+ * A sweep that learns of queries the cached listing never had must drop
+ * that listing, or the operator keeps seeing the old truncated one until
+ * its TTL happens to expire — which is the same invisible-tail defect from
+ * a different direction.
+ */
+exports.QUERY_LOG_PATH = "/net/pacs/queries";
+/**
+ * Turns one CUBE query record into an index entry.
+ *
+ * @param row - A row of the `pacs/queries` collection.
+ * @returns The entry, or null when the row carries no usable criteria.
+ */
+function queryRow_toEntry(row) {
+    const criteria = (0, queryIndex_js_1.queryCriteria_parse)(row.query);
+    if (criteria === null || Object.keys(criteria).length === 0)
+        return null;
+    const queryId = Number(row.id);
+    if (!Number.isFinite(queryId))
+        return null;
+    const answeredAt = typeof row.creation_date === "string"
+        ? row.creation_date
+        : new Date().toISOString();
+    const result = row.result;
+    return {
+        queryId,
+        server: typeof row.pacs_identifier === "string" ? row.pacs_identifier : "",
+        criteria,
+        owner: typeof row.owner_username === "string" ? row.owner_username : "",
+        answeredAt,
+        hasResult: typeof result === "string" && result.trim().length > 0,
+    };
+}
+/**
+ * Files one query record, so the next identical question finds it.
+ *
+ * Called on every query mise runs. The index is then correct for anything
+ * this session did without the sweep having reached that far.
+ *
+ * @param row - The query record as CUBE returned it.
+ */
+function queryIndex_note(row) {
+    const entry = queryRow_toEntry(row);
+    if (entry === null)
+        return;
+    (0, queryIndex_js_1.queryIndex_get)().entry_note(entry);
+}
+/**
+ * Walks the query collection into the index.
+ *
+ * Newest first, resuming from the index's floor, until the collection is
+ * exhausted. Filters server-side by owner and status where those are given,
+ * since a query someone else asked, or one that failed, can never answer
+ * this identity's question.
+ *
+ * @param options - Server-side narrowing, typically owner and status.
+ * @returns What the sweep filed, or Err with the reason on the stack.
+ */
+async function queryIndex_sweep(options = {}) {
+    const index = (0, queryIndex_js_1.queryIndex_get)();
+    // A restored index has already walked everything down to its floor, so
+    // the only records it can be missing are the ones that arrived since.
+    // Asking for those alone turns a rebuild into a top-up — which is the
+    // whole reason the index is persisted rather than swept every boot.
+    const newest = index.newest_get();
+    const resume = newest === null ? {} : { min_creation_date: newest };
+    let offset = 0;
+    let pages = 0;
+    let indexed = 0;
+    let oldest = null;
+    while (pages < exports.QUERY_SWEEP_PAGE_MAX) {
+        const page = await (0, chrisPACS_js_1.pacsQueries_list)({
+            ...resume,
+            ...options,
+            limit: exports.QUERY_SWEEP_PAGE,
+            offset,
+        });
+        if (!page.ok) {
+            errorStack_js_1.errorStack.stack_push("error", "PACS query sweep: could not read the query collection");
+            return (0, result_js_1.Err)();
+        }
+        const rows = page.value?.tableData ?? [];
+        pages += 1;
+        for (const row of rows) {
+            const entry = queryRow_toEntry(row);
+            if (entry === null)
+                continue;
+            index.entry_note(entry);
+            indexed += 1;
+            if (oldest === null || Date.parse(entry.answeredAt) < Date.parse(oldest)) {
+                oldest = entry.answeredAt;
+            }
+        }
+        // A short page is the collection's own end marker.
+        if (rows.length < exports.QUERY_SWEEP_PAGE) {
+            if (oldest !== null)
+                index.floor_set(oldest);
+            if (indexed > 0)
+                (0, listCache_js_1.listCache_get)().cache_invalidate(exports.QUERY_LOG_PATH);
+            return (0, result_js_1.Ok)({ indexed, pages, bounded: false, resumed: newest !== null });
+        }
+        offset += rows.length;
+    }
+    if (oldest !== null)
+        index.floor_set(oldest);
+    if (indexed > 0)
+        (0, listCache_js_1.listCache_get)().cache_invalidate(exports.QUERY_LOG_PATH);
+    return (0, result_js_1.Ok)({ indexed, pages, bounded: true, resumed: newest !== null });
+}
+//# sourceMappingURL=queryIndexSweep.js.map

package/dist/pacs/queryIndexSweep.js.map

@@ -0,0 +1 @@
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package/dist/resources/chrisResources.d.ts

@@ -57,6 +57,18 @@ export interface FilteredResourceData {
     selectedFields: string[];
     /** Total count of items in the full collection (may exceed tableData.length when paginated). */
     totalCount?: number;
+    /**
+     * Set when the walk could not finish — a page the server refused, or a
+     * bound the caller asked for and the collection exceeded. A listing that
+     * is short must say so; a surface that renders `tableData` without
+     * reading this is showing a page and calling it the answer.
+     */
+    incomplete?: {
+        /** How many were gathered before it stopped. */
+        gathered: number;
+        /** Why it stopped, in words a surface can render. */
+        reason: string;
+    };
 }
 /**
  * A dictionary with string keys and primitive values.

package/dist/resources/chrisResources.js

@@ -14,6 +14,17 @@ const adapter_js_1 = require("../chrisapi/adapter.js");
 const chrisConnection_js_1 = require("../connect/chrisConnection.js");
 const config_js_1 = require("../config/config.js");
 const errorStack_js_1 = require("../error/errorStack.js");
+/**
+ * A dictionary with string keys and primitive values.
+ */
+/**
+ * How many records a page asks for.
+ *
+ * One number for every walk in this class: the paging loop and the bounded
+ * default read the same constant, so a page size cannot drift between the
+ * thing that walks and the thing that stops.
+ */
+const PAGE_SIZE = 100;
 /**
  * Base class for managing ChRIS resources.
  */
@@ -154,15 +165,30 @@ class ChRISResource {
      * @returns A Promise resolving to FilteredResourceData containing all matching resources, or null.
      */
     async resources_getAll(options) {
-        const limit = 100;
+        const limit = PAGE_SIZE;
         let offset = 0;
         let allTableData = [];
         let selectedFields = [];
         // If options has a limit, we should respect it? No, getAll implies fetching everything.
         // But we should respect filters.
+        let stopped = null;
         while (true) {
             const pageOptions = { ...options, limit, offset };
-            const result = await this.resources_listAndFilterByOptions(pageOptions);
+            let result;
+            try {
+                result = this.resources_filterByFields(await this.resourceFields_get(await this.resources_getList(pageOptions)));
+            }
+            catch (error) {
+                // A walk that never started is a FAILED listing and stays a failure:
+                // callers check for one. A walk that started and then hit a page the
+                // server refused keeps its rows and says where it stopped — CUBE is
+                // known to fail some queries beyond a certain offset, and a short
+                // answer that reads as a complete one is the defect this fixes.
+                if (allTableData.length === 0)
+                    throw error;
+                stopped = error instanceof Error ? error.message : String(error);
+                break;
+            }
             if (!result || !result.tableData) {
                 break;
             }
@@ -193,6 +219,12 @@ class ChRISResource {
             tableData: allTableData,
             selectedFields,
             totalCount: allTableData.length,
+            ...(stopped === null ? {} : {
+                incomplete: {
+                    gathered: allTableData.length,
+                    reason: `stopped after ${allTableData.length}: ${stopped}`,
+                },
+            }),
         };
     }
     /**
@@ -201,11 +233,24 @@ class ChRISResource {
      * @returns A Promise resolving to filtered resource data or null.
      */
     async resources_listAndFilterByOptions(options) {
+        // No limit named means the whole collection: walk it. A caller that
+        // names one has asked a bounded question and gets exactly that page,
+        // marked short when the collection is bigger than the bound — a listing
+        // shows what is there, or says what it is not showing (#401).
+        if (options?.limit === undefined) {
+            return await this.resources_getAll(options);
+        }
         const results = this.resources_filterByFields(await this.resourceFields_get(await this.resources_getList(options)));
         if (results && (0, adapter_js_1.resource_isList)(this._resourceCollection)) {
             const total = this._resourceCollection.totalCount;
             if (total >= 0)
                 results.totalCount = total;
+            if (total > results.tableData.length) {
+                results.incomplete = {
+                    gathered: results.tableData.length,
+                    reason: `showing ${results.tableData.length} of ${total} — the caller asked for ${options.limit}`,
+                };
+            }
         }
         return results;
     }
@@ -341,8 +386,13 @@ class ChRISResource {
         return filteredItems.length > 0 ? filteredItems : null;
     }
     async resources_getList(options, resourceMethod) {
+        // A caller that named no bound is asking for the collection, not for the
+        // first twenty of it. The default that used to sit here answered a
+        // different question than the one asked (#401), and said nothing about
+        // the difference. `resources_getAll` pages explicitly and passes its own
+        // limit, so it is unaffected.
         const params = {
-            limit: 20,
+            limit: PAGE_SIZE,
             offset: 0,
             ...options,
         };