@fnndsc/cumin 3.2.4

package/LICENSE

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+MIT License
+
+Copyright (c) 2024 FNNDSC / BCH
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+```
+  ____                _
+ / ___|   _ ___  ____(_)_ __
+| |  | | | | '_ \| '_ \| '_ \
+| |__| |_| | | | | | | | | | |
+ \____\__,_|_| |_|_| |_|_| |_|
+```
+**Cumin Underpins Management Infrastructure Needs**
+
+`cumin` is the infrastructure and state management layer of the ChRIS interface ecosystem. It is a backend library that handles the "dirty work" of connecting to ChRIS, managing authentication tokens, and persisting user sessions.
+
+## Installation
+
+```bash
+npm install @fnndsc/cumin
+```
+
+Requires Node.js ≥ 20.12. Ships with TypeScript type definitions.
+
+## Usage
+
+```typescript
+import { ChRISConnection, ChrisContext, ChrisIO } from "@fnndsc/cumin";
+
+// The context engine remembers the active user, CUBE URL, and working directory
+const context = new ChrisContext();
+await context.init();
+const cubeURL: string | null = await context.ChRISURL_get();
+```
+
+See [Core Features](#core-features) for the full API surface.
+
+## Abstract
+
+`cumin` abstracts the ChRIS REST API into a stateful, object-oriented environment. It is responsible for:
+1.  **Connection Management**: Handling authentication, token storage, and client initialization.
+2.  **Context Persistence**: Implementing the "Context" engine that remembers the active User, CUBE URL, and Working Directory.
+3.  **IO & Storage**: Providing an abstraction (`IStorageProvider`) for filesystem access, enabling support for both Node.js (via `fs`) and other environments.
+
+## Role in the Ecosystem
+
+In the "Sandwich Model" architecture, `cumin` is the bottom layer (just above the raw API client).
+
+-   **Consumers**: Primarily [`salsa`](https://github.com/FNNDSC/salsa) (logic) and [`chili`](https://github.com/FNNDSC/chili) (CLI state).
+-   **Environment**: Designed for Node.js but architected with interfaces to support browser environments.
+
+## Core Features
+
+-   **`ChrisContext`**: The state machine for multi-tenant, multi-backend sessions.
+-   **`ChRISConnection`**: Wrapper for the low-level API client.
+-   **`IStorageProvider`**: Abstraction interface for reading/writing config and data.
+    -   Includes `readBinary` for binary file uploads.
+    -   Includes recursive directory traversal helpers.
+-   **`ChrisIO`**: High-level IO operations, including recursive directory uploading (`uploadLocalPath`).
+-   **`ChRISResource.resources_getAll()`**: Generic pagination handler.
+-   **`ListCache`** (`listCache_get()`): Session-scoped directory listing cache for the VFS.
+-   **`ProcCache`** (`procCache_get()`): Session-scoped job monitoring cache. Stores all visible plugin instances as a DAG (two flat maps: `instances` keyed by ID, `children`/`feedRoots` for tree traversal). Structure is permanent once built; only non-terminal instance statuses are refreshed on read. Powers the `/proc/feeds/` VFS provider in salsa.
+
+## Developer Setup
+
+To build the `cumin` library from source:
+
+1.  **Install dependencies:**
+    ```bash
+    npm install
+    ```
+
+2.  **Compile:**
+    ```bash
+    npm run build
+    ```
+
+## License
+
+MIT — part of the [ChRIS Project](https://chrisproject.org).
+
+---
+_-30-_

package/dist/activities/chrisActivity.d.ts

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+/**
+ * @file ChRIS Activity
+ *
+ * This module defines the base Activity class for interactions with ChRIS.
+ *
+ * @module
+ */
+import Client from "@fnndsc/chrisapi";
+/**
+ * Base class for ChRIS activities.
+ */
+export declare class Activity {
+    constructor();
+    /**
+     * Retrieves the ChRIS client instance asynchronously.
+     * @returns A Promise resolving to the Client instance or null.
+     */
+    client_get(): Promise<Client | null>;
+}

package/dist/activities/chrisActivity.js

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+"use strict";
+/**
+ * @file ChRIS Activity
+ *
+ * This module defines the base Activity class for interactions with ChRIS.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Activity = void 0;
+const chrisConnection_js_1 = require("../connect/chrisConnection.js");
+/**
+ * Base class for ChRIS activities.
+ */
+class Activity {
+    // private _client: Client | null = null; // No longer needed
+    constructor() {
+        // Client is fetched lazily
+    }
+    /**
+     * Retrieves the ChRIS client instance asynchronously.
+     * @returns A Promise resolving to the Client instance or null.
+     */
+    async client_get() {
+        return await chrisConnection_js_1.chrisConnection.client_get();
+    }
+}
+exports.Activity = Activity;
+//# sourceMappingURL=chrisActivity.js.map

package/dist/activities/chrisActivity.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"chrisActivity.js","sourceRoot":"","sources":["../../src/activities/chrisActivity.ts"],"names":[],"mappings":";AAAA;;;;;;GAMG;;;AAGH,sEAAgE;AAEhE;;GAEG;AACH,MAAa,QAAQ;IACnB,6DAA6D;IAE7D;QACE,2BAA2B;IAC7B,CAAC;IAED;;;OAGG;IACI,KAAK,CAAC,UAAU;QACrB,OAAO,MAAM,oCAAe,CAAC,UAAU,EAAE,CAAC;IAC5C,CAAC;CACF;AAdD,4BAcC"}

package/dist/cache/index.d.ts

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+/**
+ * @file Cache module exports.
+ *
+ * @module
+ */
+export { ListCache, listCache_get } from './listCache.js';
+export type { CacheStats, CacheResult, CacheOptions } from './listCache.js';
+export { ProcCache, procCache_get } from './procCache.js';
+export type { ProcInstance, ProcFeed, ProcWarmupProgress } from './procCache.js';

package/dist/cache/index.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.procCache_get = exports.ProcCache = exports.listCache_get = exports.ListCache = void 0;
+/**
+ * @file Cache module exports.
+ *
+ * @module
+ */
+var listCache_js_1 = require("./listCache.js");
+Object.defineProperty(exports, "ListCache", { enumerable: true, get: function () { return listCache_js_1.ListCache; } });
+Object.defineProperty(exports, "listCache_get", { enumerable: true, get: function () { return listCache_js_1.listCache_get; } });
+var procCache_js_1 = require("./procCache.js");
+Object.defineProperty(exports, "ProcCache", { enumerable: true, get: function () { return procCache_js_1.ProcCache; } });
+Object.defineProperty(exports, "procCache_get", { enumerable: true, get: function () { return procCache_js_1.procCache_get; } });
+//# sourceMappingURL=index.js.map

package/dist/cache/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cache/index.ts"],"names":[],"mappings":";;;AAAA;;;;GAIG;AACH,+CAA0D;AAAjD,yGAAA,SAAS,OAAA;AAAE,6GAAA,aAAa,OAAA;AAEjC,+CAA0D;AAAjD,yGAAA,SAAS,OAAA;AAAE,6GAAA,aAAa,OAAA"}

package/dist/cache/listCache.d.ts

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+/**
+ * @file Enhanced Directory Listing Cache with TTL and dirty tracking.
+ *
+ * Provides a singleton cache for directory listings to avoid redundant API calls
+ * during tab completion and file operations. Features:
+ * - TTL-based expiration (different TTLs per path pattern)
+ * - Dirty flag tracking (local mutations mark cache as needing refresh)
+ * - LRU eviction (bounded memory usage)
+ * - Optimistic serving (serve stale cache while refreshing)
+ *
+ * Generic implementation - stores any data type keyed by path.
+ *
+ * @module
+ */
+/**
+ * Result returned by cache_get with freshness information.
+ */
+export interface CacheResult<T = unknown> {
+    /** The cached data */
+    data: T;
+    /** True if within TTL and not dirty */
+    fresh: boolean;
+    /** Age in milliseconds */
+    age: number;
+}
+/**
+ * Options for cache_set.
+ */
+export interface CacheOptions {
+    /** Override default TTL for this entry (milliseconds) */
+    ttl?: number;
+    /** Mark as dirty immediately */
+    dirty?: boolean;
+}
+/**
+ * Statistics about cache usage.
+ */
+export interface CacheStats {
+    /** Total number of cache hits (fresh). */
+    hits: number;
+    /** Total number of cache misses. */
+    misses: number;
+    /** Total number of stale hits (served but expired). */
+    staleHits: number;
+    /** Number of LRU evictions. */
+    evictions: number;
+    /** Number of entries currently in cache. */
+    entries: number;
+    /** Estimated total memory usage in bytes. */
+    totalSize: number;
+}
+/**
+ * Singleton cache for directory listings with TTL and dirty tracking.
+ *
+ * Generic cache that stores any data type keyed by path. Eliminates redundant
+ * API calls by caching directory contents after ls operations.
+ *
+ * Enhanced features:
+ * - TTL-based expiration: Different paths have different TTLs
+ * - Dirty flag tracking: Local mutations mark cache as needing refresh
+ * - LRU eviction: Bounded memory usage
+ * - Optimistic serving: Serve stale cache immediately, refresh in background
+ *
+ * Usage:
+ * ```typescript
+ * const cache = listCache_get();
+ *
+ * // Check cache (returns CacheResult with freshness info)
+ * const cached = cache.cache_get("/PUBLIC");
+ * if (cached) {
+ *   console.log(cached.data);  // Show immediately
+ *   if (!cached.fresh) {
+ *     console.log('Refreshing...');
+ *     // Fetch fresh data in background
+ *   }
+ * }
+ *
+ * // Store data
+ * cache.cache_set("/PUBLIC", items);
+ *
+ * // Mark dirty after mutation
+ * cache.cache_markDirty("/home/user");
+ *
+ * // Optimistic update
+ * cache.cache_update("/home/user", (items) => items.filter(i => i.name !== 'deleted.txt'));
+ * ```
+ */
+export declare class ListCache {
+    private static instance;
+    /** Cache storage: path → entry. */
+    private cache;
+    /** Maximum cache entries (LRU eviction). */
+    private maxEntries;
+    /** Default TTL for unconfigured paths (3 minutes). */
+    private defaultTTL;
+    /** Path-specific TTL configuration. */
+    private ttlConfig;
+    /** Cache statistics. */
+    private stats;
+    /**
+     * Private constructor to enforce singleton pattern.
+     */
+    private constructor();
+    /**
+     * Gets the singleton instance of ListCache.
+     *
+     * @returns The ListCache singleton instance.
+     */
+    static instance_get(): ListCache;
+    /**
+     * Retrieves data from cache with freshness information.
+     *
+     * @param path - The path to retrieve.
+     * @returns CacheResult with freshness info, or null if not cached.
+     */
+    cache_get<T = unknown>(path: string): CacheResult<T> | null;
+    /**
+     * Stores data in cache with optional TTL override.
+     *
+     * @param path - The path to cache.
+     * @param data - The data to cache.
+     * @param options - Optional TTL and dirty flag.
+     */
+    cache_set<T = unknown>(path: string, data: T, options?: CacheOptions): void;
+    /**
+     * Marks a cached path as dirty (needs refresh).
+     * Used when local mutations might have changed the data.
+     *
+     * @param path - The path to mark dirty.
+     */
+    cache_markDirty(path: string): void;
+    /**
+     * Optimistically updates cache after a mutation.
+     * Example: After rm, remove item from parent directory cache.
+     *
+     * @param path - The parent directory path.
+     * @param updater - Function to transform cached data.
+     */
+    cache_update<T = unknown>(path: string, updater: (data: T) => T): void;
+    /**
+     * Invalidates cache for a specific path or clears entire cache.
+     * Called by file operations that modify directory contents (mkdir, touch, rm, upload).
+     *
+     * @param path - Optional specific path to invalidate. If omitted, clears entire cache.
+     */
+    cache_invalidate(path?: string): void;
+    /**
+     * @deprecated Use cache without cwd tracking. Cache persists across navigation.
+     * This method is kept for backward compatibility but does nothing.
+     *
+     * @param _newCwd - Ignored.
+     */
+    cwd_update(_newCwd: string): void;
+    /**
+     * Gets TTL for a specific path based on configuration.
+     *
+     * @param path - The path to get TTL for.
+     * @returns TTL in milliseconds.
+     */
+    private ttl_get;
+    /**
+     * Evicts oldest entries if cache exceeds max size.
+     */
+    private evict_lru;
+    /**
+     * Gets cache statistics.
+     *
+     * @returns Cache statistics including hits, misses, and current state.
+     */
+    stats_get(): CacheStats;
+    /**
+     * Resets cache statistics.
+     * Useful for testing and monitoring.
+     */
+    stats_reset(): void;
+}
+/**
+ * Convenience function to get the ListCache singleton instance.
+ *
+ * @returns The ListCache singleton instance.
+ */
+export declare function listCache_get(): ListCache;

package/dist/cache/listCache.js

@@ -0,0 +1,266 @@
+"use strict";
+/**
+ * @file Enhanced Directory Listing Cache with TTL and dirty tracking.
+ *
+ * Provides a singleton cache for directory listings to avoid redundant API calls
+ * during tab completion and file operations. Features:
+ * - TTL-based expiration (different TTLs per path pattern)
+ * - Dirty flag tracking (local mutations mark cache as needing refresh)
+ * - LRU eviction (bounded memory usage)
+ * - Optimistic serving (serve stale cache while refreshing)
+ *
+ * Generic implementation - stores any data type keyed by path.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ListCache = void 0;
+exports.listCache_get = listCache_get;
+/**
+ * Singleton cache for directory listings with TTL and dirty tracking.
+ *
+ * Generic cache that stores any data type keyed by path. Eliminates redundant
+ * API calls by caching directory contents after ls operations.
+ *
+ * Enhanced features:
+ * - TTL-based expiration: Different paths have different TTLs
+ * - Dirty flag tracking: Local mutations mark cache as needing refresh
+ * - LRU eviction: Bounded memory usage
+ * - Optimistic serving: Serve stale cache immediately, refresh in background
+ *
+ * Usage:
+ * ```typescript
+ * const cache = listCache_get();
+ *
+ * // Check cache (returns CacheResult with freshness info)
+ * const cached = cache.cache_get("/PUBLIC");
+ * if (cached) {
+ *   console.log(cached.data);  // Show immediately
+ *   if (!cached.fresh) {
+ *     console.log('Refreshing...');
+ *     // Fetch fresh data in background
+ *   }
+ * }
+ *
+ * // Store data
+ * cache.cache_set("/PUBLIC", items);
+ *
+ * // Mark dirty after mutation
+ * cache.cache_markDirty("/home/user");
+ *
+ * // Optimistic update
+ * cache.cache_update("/home/user", (items) => items.filter(i => i.name !== 'deleted.txt'));
+ * ```
+ */
+class ListCache {
+    /**
+     * Private constructor to enforce singleton pattern.
+     */
+    constructor() {
+        /** Cache storage: path → entry. */
+        this.cache = new Map();
+        /** Maximum cache entries (LRU eviction). */
+        this.maxEntries = 100;
+        /** Default TTL for unconfigured paths (3 minutes). */
+        this.defaultTTL = 3 * 60 * 1000;
+        /** Path-specific TTL configuration. */
+        this.ttlConfig = new Map([
+            ['/PUBLIC', 10 * 60 * 1000], // 10 min (stable, public directory)
+            ['/home', 5 * 60 * 1000], // 5 min (user home directories)
+            ['/bin', 60 * 60 * 1000], // 1 hour (plugins rarely change)
+            ['/feeds/*', 5 * 60 * 1000], // 5 min (feed outputs)
+        ]);
+        /** Cache statistics. */
+        this.stats = {
+            hits: 0,
+            misses: 0,
+            staleHits: 0,
+            evictions: 0,
+        };
+    }
+    /**
+     * Gets the singleton instance of ListCache.
+     *
+     * @returns The ListCache singleton instance.
+     */
+    static instance_get() {
+        if (!ListCache.instance) {
+            ListCache.instance = new ListCache();
+        }
+        return ListCache.instance;
+    }
+    /**
+     * Retrieves data from cache with freshness information.
+     *
+     * @param path - The path to retrieve.
+     * @returns CacheResult with freshness info, or null if not cached.
+     */
+    cache_get(path) {
+        const entry = this.cache.get(path);
+        if (!entry) {
+            this.stats.misses++;
+            return null;
+        }
+        // LRU: Move to end (mark as recently used)
+        this.cache.delete(path);
+        this.cache.set(path, entry);
+        // Calculate freshness
+        const age = Date.now() - entry.timestamp;
+        const fresh = !entry.dirty && age < entry.ttl;
+        if (fresh) {
+            this.stats.hits++;
+        }
+        else {
+            this.stats.staleHits++;
+        }
+        return { data: entry.data, fresh, age };
+    }
+    /**
+     * Stores data in cache with optional TTL override.
+     *
+     * @param path - The path to cache.
+     * @param data - The data to cache.
+     * @param options - Optional TTL and dirty flag.
+     */
+    cache_set(path, data, options) {
+        // LRU: If exists, delete and re-add (moves to end)
+        if (this.cache.has(path)) {
+            this.cache.delete(path);
+        }
+        const ttl = options?.ttl ?? this.ttl_get(path);
+        this.cache.set(path, {
+            data,
+            timestamp: Date.now(),
+            dirty: options?.dirty ?? false,
+            ttl,
+        });
+        // LRU eviction if over limit
+        this.evict_lru();
+    }
+    /**
+     * Marks a cached path as dirty (needs refresh).
+     * Used when local mutations might have changed the data.
+     *
+     * @param path - The path to mark dirty.
+     */
+    cache_markDirty(path) {
+        const entry = this.cache.get(path);
+        if (entry) {
+            entry.dirty = true;
+        }
+    }
+    /**
+     * Optimistically updates cache after a mutation.
+     * Example: After rm, remove item from parent directory cache.
+     *
+     * @param path - The parent directory path.
+     * @param updater - Function to transform cached data.
+     */
+    cache_update(path, updater) {
+        const entry = this.cache.get(path);
+        if (entry) {
+            entry.data = updater(entry.data);
+            entry.timestamp = Date.now(); // Reset timestamp
+            entry.dirty = false; // Clean after update
+        }
+    }
+    /**
+     * Invalidates cache for a specific path or clears entire cache.
+     * Called by file operations that modify directory contents (mkdir, touch, rm, upload).
+     *
+     * @param path - Optional specific path to invalidate. If omitted, clears entire cache.
+     */
+    cache_invalidate(path) {
+        if (path !== undefined) {
+            this.cache.delete(path);
+        }
+        else {
+            this.cache.clear();
+        }
+    }
+    /**
+     * @deprecated Use cache without cwd tracking. Cache persists across navigation.
+     * This method is kept for backward compatibility but does nothing.
+     *
+     * @param _newCwd - Ignored.
+     */
+    cwd_update(_newCwd) {
+        // No-op: Cache no longer flushes on directory change
+        // Kept for backward compatibility during transition
+    }
+    /**
+     * Gets TTL for a specific path based on configuration.
+     *
+     * @param path - The path to get TTL for.
+     * @returns TTL in milliseconds.
+     */
+    ttl_get(path) {
+        if (this.ttlConfig.has(path)) {
+            return this.ttlConfig.get(path);
+        }
+        for (const [pattern, ttl] of this.ttlConfig) {
+            if (pattern.includes('*')) {
+                const regex = new RegExp('^' + pattern.replace(/\*/g, '.*') + '$');
+                if (regex.test(path)) {
+                    return ttl;
+                }
+            }
+        }
+        return this.defaultTTL;
+    }
+    /**
+     * Evicts oldest entries if cache exceeds max size.
+     */
+    evict_lru() {
+        while (this.cache.size > this.maxEntries) {
+            const oldestKey = this.cache.keys().next().value;
+            if (oldestKey !== undefined) {
+                this.cache.delete(oldestKey);
+                this.stats.evictions++;
+            }
+            else {
+                break; // Should never happen, but safety check
+            }
+        }
+    }
+    /**
+     * Gets cache statistics.
+     *
+     * @returns Cache statistics including hits, misses, and current state.
+     */
+    stats_get() {
+        let totalSize = 0;
+        for (const entry of this.cache.values()) {
+            // Rough estimate: JSON string length
+            totalSize += JSON.stringify(entry.data).length;
+        }
+        return {
+            hits: this.stats.hits,
+            misses: this.stats.misses,
+            staleHits: this.stats.staleHits,
+            evictions: this.stats.evictions,
+            entries: this.cache.size,
+            totalSize,
+        };
+    }
+    /**
+     * Resets cache statistics.
+     * Useful for testing and monitoring.
+     */
+    stats_reset() {
+        this.stats.hits = 0;
+        this.stats.misses = 0;
+        this.stats.staleHits = 0;
+        this.stats.evictions = 0;
+    }
+}
+exports.ListCache = ListCache;
+/**
+ * Convenience function to get the ListCache singleton instance.
+ *
+ * @returns The ListCache singleton instance.
+ */
+function listCache_get() {
+    return ListCache.instance_get();
+}
+//# sourceMappingURL=listCache.js.map

package/dist/cache/listCache.js.map

@@ -0,0 +1 @@
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