@fnndsc/salsa 3.2.4

package/dist/vfs/providers/proc.js

@@ -0,0 +1,478 @@
+"use strict";
+/**
+ * @file /proc VFS Provider
+ *
+ * Surfaces ChRIS plugin instances as a navigable DAG under /proc/jobs/.
+ * Backed by ProcCache (topology only — no status stored).
+ *
+ * Status is always fetched live:
+ * - cat .../status        → getPluginInstance(id)
+ * - ls -l /proc/jobs/N   → jobs_statusBatch(allNodeIDs) — parallel
+ * - ls /proc/jobs        → aggregate from ProcFeed job counters (no API)
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ProcVfsProvider = void 0;
+exports.feedStatus_derive = feedStatus_derive;
+exports.procPath_parse = procPath_parse;
+exports.procFeed_ensureLoaded = procFeed_ensureLoaded;
+exports.procTopology_warmup = procTopology_warmup;
+exports.procCache_refresh = procCache_refresh;
+const cumin_1 = require("@fnndsc/cumin");
+const index_js_1 = require("../../jobs/index.js");
+/** Virtual filenames inside each instance directory. */
+const INSTANCE_FILES = new Set(['status', 'params', 'log']);
+/** Virtual filenames inside each feed directory. */
+const FEED_FILES = new Set(['status', 'title']);
+const PAGE = 100;
+// ── Cache build ────────────────────────────────────────────────────────────
+/**
+ * Builds the feed index (fast). Fetches all feeds with job counters.
+ * Instance topology is loaded separately via procTopology_warmup().
+ */
+async function procCache_build() {
+    const cache = (0, cumin_1.procCache_get)();
+    cache.cache_clear();
+    const client = await cumin_1.chrisConnection.client_get();
+    if (!client) {
+        cumin_1.errorStack.stack_push('error', 'procCache_build: not connected');
+        return;
+    }
+    const typedClient = client;
+    let feedOffset = 0;
+    while (true) {
+        const feedPage = await typedClient.getFeeds({ limit: PAGE, offset: feedOffset });
+        const chunk = feedPage.data ?? [];
+        for (const f of chunk) {
+            cache.feed_add({
+                id: Number(f.id),
+                title: String(f.name),
+                creationDate: String(f.creation_date ?? ''),
+                finishedJobs: Number(f.finished_jobs ?? 0),
+                erroredJobs: Number(f.errored_jobs ?? 0),
+                startedJobs: Number(f.started_jobs ?? 0),
+                scheduledJobs: Number(f.scheduled_jobs ?? 0),
+                cancelledJobs: Number(f.cancelled_jobs ?? 0),
+                createdJobs: Number(f.created_jobs ?? 0),
+            });
+        }
+        if (chunk.length < PAGE)
+            break;
+        feedOffset += PAGE;
+    }
+    cache.built_set();
+}
+/** Ensures the feed index is built, building it on first access. */
+async function cache_ensure() {
+    if (!(0, cumin_1.procCache_get)().built) {
+        await procCache_build();
+    }
+}
+/**
+ * Loads instance topology for a single feed.
+ * Uses in-flight map to prevent duplicate API calls.
+ */
+async function feedInstances_load(feedID) {
+    const cache = (0, cumin_1.procCache_get)();
+    const client = await cumin_1.chrisConnection.client_get();
+    if (!client)
+        return;
+    const typedClient = client;
+    const instances = [];
+    let offset = 0;
+    while (true) {
+        const page = await typedClient.getPluginInstances({
+            feed_id: feedID, limit: PAGE, offset,
+        });
+        const chunk = page.data ?? [];
+        instances.push(...chunk);
+        if (chunk.length < PAGE)
+            break;
+        offset += PAGE;
+    }
+    for (const inst of instances) {
+        const prevID = (inst.previous_id !== null && inst.previous_id !== undefined)
+            ? Number(inst.previous_id)
+            : null;
+        cache.instance_add({
+            id: Number(inst.id),
+            feedID: Number(inst.feed_id),
+            parentID: prevID,
+            pluginName: String(inst.plugin_name),
+            params: null,
+        });
+    }
+    cache.topologyLoaded_mark(feedID);
+}
+/**
+ * Ensures topology for a feed is loaded.
+ * Per-feed loads proceed immediately even while the global sweep is running —
+ * instance_add is idempotent so concurrent additions are safe.
+ */
+async function feedInstances_ensureLoaded(feedID) {
+    const cache = (0, cumin_1.procCache_get)();
+    if (cache.topologyLoaded_has(feedID))
+        return;
+    const inflight = cache.loading_get(feedID);
+    if (inflight)
+        return inflight;
+    const promise = feedInstances_load(feedID);
+    cache.loading_set(feedID, promise);
+    await promise;
+    cache.loading_clear(feedID);
+}
+// ── Aggregate status ───────────────────────────────────────────────────────
+/** Derives aggregate feed status from stored job counters — no API call. */
+function feedStatus_derive(feed) {
+    if (feed.erroredJobs > 0)
+        return 'finishedWithError';
+    const running = feed.startedJobs + feed.scheduledJobs + feed.createdJobs;
+    if (running > 0)
+        return 'running';
+    if (feed.cancelledJobs > 0 && feed.finishedJobs === 0)
+        return 'cancelled';
+    if (feed.finishedJobs > 0)
+        return 'finishedSuccessfully';
+    return 'empty';
+}
+// ── Path parsing ───────────────────────────────────────────────────────────
+function procPath_parse(pathStr) {
+    const parts = pathStr.replace(/^\/proc\/feeds\/?/, '').split('/').filter(Boolean);
+    let feedID = null;
+    let instanceID = null;
+    let virtualFile = null;
+    if (parts.length >= 1) {
+        const feedMatch = parts[0].match(/^feed_(\d+)$/);
+        if (feedMatch)
+            feedID = parseInt(feedMatch[1], 10);
+    }
+    if (parts.length >= 2) {
+        const lastPart = parts[parts.length - 1];
+        if (FEED_FILES.has(lastPart) || INSTANCE_FILES.has(lastPart)) {
+            virtualFile = lastPart;
+            if (parts.length >= 3) {
+                const instMatch = parts[parts.length - 2].match(/_(\d+)$/);
+                if (instMatch)
+                    instanceID = parseInt(instMatch[1], 10);
+            }
+        }
+        else {
+            const instMatch = lastPart.match(/_(\d+)$/);
+            if (instMatch)
+                instanceID = parseInt(instMatch[1], 10);
+        }
+    }
+    return { feedID, instanceID, virtualFile };
+}
+/** Formats instance params as key=value lines. */
+function params_render(inst) {
+    if (!inst.params || Object.keys(inst.params).length === 0)
+        return '(no parameters)';
+    return Object.entries(inst.params)
+        .map(([k, v]) => `${k}=${String(v)}`)
+        .join('\n');
+}
+/** Collects all instance IDs for a feed recursively. */
+function getAllInstanceIDs_forFeed(feedID, cache) {
+    const result = [];
+    const queue = [...cache.feedRoots_get(feedID)];
+    while (queue.length > 0) {
+        const id = queue.shift();
+        result.push(id);
+        queue.push(...cache.children_get(id));
+    }
+    return result;
+}
+// ── Provider ───────────────────────────────────────────────────────────────
+/**
+ * VFS provider exposing running jobs and feeds under the /proc namespace.
+ */
+class ProcVfsProvider {
+    prefix = '/proc/jobs';
+    async list(pathStr, _options) {
+        await cache_ensure();
+        const cache = (0, cumin_1.procCache_get)();
+        const clean = pathStr.replace(/\/$/, '');
+        // /proc/jobs — list all feeds with aggregate status from counters
+        if (clean === '/proc/jobs') {
+            const items = cache.feedIDs_get().map((feedID) => {
+                const feed = cache.feed_get(feedID);
+                const status = feed ? feedStatus_derive(feed) : 'unknown';
+                return {
+                    name: `feed_${feedID}`,
+                    type: 'job',
+                    size: 0,
+                    owner: '',
+                    date: '',
+                    title: feed?.title ?? `feed_${feedID}`,
+                    status,
+                };
+            });
+            return (0, cumin_1.Ok)(items);
+        }
+        const { feedID, instanceID } = procPath_parse(clean);
+        // /proc/jobs/feed_N — list root instances + feed virtual files
+        if (feedID !== null && instanceID === null) {
+            await feedInstances_ensureLoaded(feedID);
+            const feed = cache.feed_get(feedID);
+            if (!feed)
+                return (0, cumin_1.Ok)([]);
+            // Collect all root instance IDs to batch-fetch statuses
+            const rootIDs = cache.feedRoots_get(feedID);
+            const statuses = rootIDs.length > 0
+                ? await (0, index_js_1.jobs_statusBatch)(rootIDs)
+                : new Map();
+            const items = [];
+            items.push({ name: 'status', type: 'file', size: 0, owner: '', date: '' });
+            items.push({ name: 'title', type: 'file', size: 0, owner: '', date: '' });
+            for (const rootID of rootIDs) {
+                const inst = cache.instance_get(rootID);
+                if (!inst)
+                    continue;
+                items.push({
+                    name: `${inst.pluginName}_${rootID}`,
+                    type: 'job',
+                    size: 0,
+                    owner: '',
+                    date: '',
+                    status: statuses.get(rootID) ?? 'unknown',
+                });
+            }
+            return (0, cumin_1.Ok)(items);
+        }
+        // /proc/jobs/feed_N/plugin_ID — list children + virtual files
+        if (feedID !== null && instanceID !== null) {
+            await feedInstances_ensureLoaded(feedID);
+            const inst = cache.instance_get(instanceID);
+            if (!inst)
+                return (0, cumin_1.Ok)([]);
+            const childIDs = cache.children_get(instanceID);
+            const statuses = childIDs.length > 0
+                ? await (0, index_js_1.jobs_statusBatch)(childIDs)
+                : new Map();
+            const items = [];
+            items.push({ name: 'status', type: 'file', size: 0, owner: '', date: '' });
+            items.push({ name: 'params', type: 'file', size: 0, owner: '', date: '' });
+            items.push({ name: 'log', type: 'file', size: 0, owner: '', date: '' });
+            for (const childID of childIDs) {
+                const child = cache.instance_get(childID);
+                if (!child)
+                    continue;
+                items.push({
+                    name: `${child.pluginName}_${childID}`,
+                    type: 'job',
+                    size: 0,
+                    owner: '',
+                    date: '',
+                    status: statuses.get(childID) ?? 'unknown',
+                });
+            }
+            return (0, cumin_1.Ok)(items);
+        }
+        return (0, cumin_1.Ok)([]);
+    }
+    async read(pathStr) {
+        await cache_ensure();
+        const cache = (0, cumin_1.procCache_get)();
+        const clean = pathStr.replace(/\/$/, '');
+        const { feedID, instanceID, virtualFile } = procPath_parse(clean);
+        // Feed-level virtual files
+        if (feedID !== null && instanceID === null && virtualFile !== null) {
+            const feed = cache.feed_get(feedID);
+            if (!feed)
+                return (0, cumin_1.Ok)('');
+            if (virtualFile === 'status')
+                return (0, cumin_1.Ok)(feedStatus_derive(feed));
+            if (virtualFile === 'title')
+                return (0, cumin_1.Ok)(feed.title);
+            return (0, cumin_1.Ok)('');
+        }
+        // Instance-level virtual files — all live or cached-on-first-read
+        if (instanceID !== null && virtualFile !== null) {
+            await feedInstances_ensureLoaded(feedID);
+            const inst = cache.instance_get(instanceID);
+            if (!inst)
+                return (0, cumin_1.Ok)('');
+            if (virtualFile === 'status') {
+                const fresh = await (0, index_js_1.job_statusFetch)(instanceID);
+                return (0, cumin_1.Ok)(fresh.ok ? fresh.value : 'unknown');
+            }
+            if (virtualFile === 'params') {
+                if (inst.params === null) {
+                    // Fetch params on first read and cache permanently
+                    const client = await cumin_1.chrisConnection.client_get();
+                    if (client) {
+                        try {
+                            const raw = await client.getPluginInstance(instanceID);
+                            if (raw?.data) {
+                                const p = { ...raw.data };
+                                delete p['id'];
+                                delete p['feed_id'];
+                                delete p['plugin_name'];
+                                delete p['status'];
+                                delete p['previous_id'];
+                                cache.params_update(instanceID, p);
+                            }
+                        }
+                        catch { /* leave null */ }
+                    }
+                }
+                return (0, cumin_1.Ok)(params_render(inst));
+            }
+            if (virtualFile === 'log') {
+                const logResult = await (0, index_js_1.job_logFetch)(instanceID);
+                return (0, cumin_1.Ok)(logResult.ok ? logResult.value : '(log unavailable)');
+            }
+        }
+        return (0, cumin_1.Ok)('');
+    }
+    async rm(pathStr, _options) {
+        await cache_ensure();
+        const cache = (0, cumin_1.procCache_get)();
+        const clean = pathStr.replace(/\/$/, '');
+        const { feedID, instanceID } = procPath_parse(clean);
+        if (feedID !== null && instanceID === null) {
+            const allIDs = getAllInstanceIDs_forFeed(feedID, cache);
+            const statusMap = await (0, index_js_1.jobs_statusBatch)(allIDs);
+            await Promise.all(allIDs.map(async (id) => {
+                const s = statusMap.get(id) ?? '';
+                if (!['finishedSuccessfully', 'finishedWithError', 'cancelled'].includes(s)) {
+                    await (0, index_js_1.job_cancel)(id);
+                }
+            }));
+            cache.feed_remove(feedID);
+            return true;
+        }
+        if (instanceID !== null) {
+            const statusResult = await (0, index_js_1.job_statusFetch)(instanceID);
+            const status = statusResult.ok ? statusResult.value : '';
+            const isTerminal = ['finishedSuccessfully', 'finishedWithError', 'cancelled'].includes(status);
+            let result;
+            if (!isTerminal) {
+                result = await (0, index_js_1.job_cancel)(instanceID);
+            }
+            else {
+                result = await (0, index_js_1.job_delete)(instanceID);
+                if (result.ok)
+                    cache.instance_remove(instanceID);
+            }
+            return result.ok;
+        }
+        return false;
+    }
+    async cp(_src, _dst, _options) { return false; }
+    async mv(_src, _dst) { return false; }
+    async mkdir(_pathStr) { return false; }
+    async touch(_pathStr) { return false; }
+    async upload(_localPath, _remotePath) { return false; }
+    async write(_pathStr, _content) { return false; }
+}
+exports.ProcVfsProvider = ProcVfsProvider;
+/**
+ * Ensures instance topology is loaded for a feed without clearing existing data.
+ * Use this from proc find — it respects already-loaded feeds and the in-flight map.
+ * Use procCache_refresh(feedID) only when a forced reload is desired.
+ */
+async function procFeed_ensureLoaded(feedID) {
+    const cache = (0, cumin_1.procCache_get)();
+    if (!cache.feed_get(feedID)) {
+        cache.feed_add({
+            id: feedID, title: `feed_${feedID}`, creationDate: '',
+            finishedJobs: 0, erroredJobs: 0, startedJobs: 0,
+            scheduledJobs: 0, cancelledJobs: 0, createdJobs: 0,
+        });
+    }
+    await feedInstances_ensureLoaded(feedID);
+}
+// ── Public API ─────────────────────────────────────────────────────────────
+/**
+ * Background topology warm-up — single paginated sweep of all plugin instances
+ * across all feeds. Replaces the per-feed fan-out that was O(feeds) round trips.
+ *
+ * Registers itself as the active sweep so that any concurrent
+ * feedInstances_ensureLoaded call waits for this sweep rather than launching
+ * its own per-feed API call.
+ */
+async function procTopology_warmup() {
+    await cache_ensure();
+    const cache = (0, cumin_1.procCache_get)();
+    const client = await cumin_1.chrisConnection.client_get();
+    if (!client)
+        return;
+    cache.warmup_progress(0, 0);
+    const typedClient = client;
+    let offset = 0;
+    let loaded = 0;
+    const seenFeedIDs = new Set();
+    while (true) {
+        const page = await typedClient.getPluginInstances({
+            limit: PAGE, offset,
+        });
+        const chunk = page.data ?? [];
+        for (const inst of chunk) {
+            const feedID = Number(inst.feed_id);
+            const prevID = (inst.previous_id !== null && inst.previous_id !== undefined)
+                ? Number(inst.previous_id)
+                : null;
+            if (!cache.feed_get(feedID)) {
+                cache.feed_add({
+                    id: feedID, title: `feed_${feedID}`, creationDate: '',
+                    finishedJobs: 0, erroredJobs: 0, startedJobs: 0,
+                    scheduledJobs: 0, cancelledJobs: 0, createdJobs: 0,
+                });
+            }
+            cache.instance_add({
+                id: Number(inst.id),
+                feedID,
+                parentID: prevID,
+                pluginName: String(inst.plugin_name),
+                params: null,
+            });
+            seenFeedIDs.add(feedID);
+            loaded++;
+        }
+        cache.warmup_progress(loaded, 0);
+        if (chunk.length < PAGE)
+            break;
+        offset += PAGE;
+    }
+    for (const feedID of seenFeedIDs) {
+        cache.topologyLoaded_mark(feedID);
+    }
+    cache.warmup_complete();
+}
+/**
+ * Rebuilds the ProcCache, optionally scoped to one feed.
+ */
+async function procCache_refresh(feedID) {
+    if (feedID !== undefined) {
+        const cache = (0, cumin_1.procCache_get)();
+        cache.feed_remove(feedID);
+        // Re-fetch feed metadata with job counters
+        const client = await cumin_1.chrisConnection.client_get();
+        if (client) {
+            const typedClient = client;
+            const page = await typedClient.getFeeds({ id: feedID, limit: 1, offset: 0 });
+            const f = (page.data ?? [])[0];
+            if (f) {
+                cache.feed_add({
+                    id: Number(f.id),
+                    title: String(f.name),
+                    creationDate: String(f.creation_date ?? ''),
+                    finishedJobs: Number(f.finished_jobs ?? 0),
+                    erroredJobs: Number(f.errored_jobs ?? 0),
+                    startedJobs: Number(f.started_jobs ?? 0),
+                    scheduledJobs: Number(f.scheduled_jobs ?? 0),
+                    cancelledJobs: Number(f.cancelled_jobs ?? 0),
+                    createdJobs: Number(f.created_jobs ?? 0),
+                });
+            }
+        }
+        await feedInstances_ensureLoaded(feedID);
+    }
+    else {
+        await procCache_build();
+    }
+}
+//# sourceMappingURL=proc.js.map

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

@@ -0,0 +1 @@
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package/dist/workflows/index.d.ts

@@ -0,0 +1,21 @@
+/**
+ * @file Workflow resource operations.
+ * @module
+ */
+import { FilteredResourceData, ListOptions } from '@fnndsc/cumin';
+/**
+ * Lists workflows (single page).
+ *
+ * @param options - Search and pagination options.
+ */
+export declare function workflows_list(options: ListOptions): Promise<FilteredResourceData | null>;
+/**
+ * Lists all workflows across all pages.
+ *
+ * @param options - Search options (limit/offset managed internally).
+ */
+export declare function workflows_listAll(options?: Partial<ListOptions>): Promise<FilteredResourceData | null>;
+/**
+ * Returns available field names for workflows.
+ */
+export declare function workflowFields_get(): Promise<string[] | null>;

package/dist/workflows/index.js

@@ -0,0 +1,37 @@
+"use strict";
+/**
+ * @file Workflow resource operations.
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.workflows_list = workflows_list;
+exports.workflows_listAll = workflows_listAll;
+exports.workflowFields_get = workflowFields_get;
+const cumin_1 = require("@fnndsc/cumin");
+/**
+ * Lists workflows (single page).
+ *
+ * @param options - Search and pagination options.
+ */
+async function workflows_list(options) {
+    const group = new cumin_1.ChRISWorkflowGroup();
+    return await group.asset.resources_listAndFilterByOptions(options);
+}
+/**
+ * Lists all workflows across all pages.
+ *
+ * @param options - Search options (limit/offset managed internally).
+ */
+async function workflows_listAll(options = {}) {
+    const group = new cumin_1.ChRISWorkflowGroup();
+    return await group.asset.resources_getAll(options);
+}
+/**
+ * Returns available field names for workflows.
+ */
+async function workflowFields_get() {
+    const group = new cumin_1.ChRISWorkflowGroup();
+    const result = await group.asset.resourceFields_get();
+    return result ? result.fields : null;
+}
+//# sourceMappingURL=index.js.map

package/dist/workflows/index.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,57 @@
+{
+  "name": "@fnndsc/salsa",
+  "version": "3.2.4",
+  "description": "Shared Application Logic and Service Assets for ChRIS",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/FNNDSC/salsa.git"
+  },
+  "homepage": "https://github.com/FNNDSC/salsa#readme",
+  "bugs": {
+    "url": "https://github.com/FNNDSC/salsa/issues"
+  },
+  "keywords": [
+    "chris",
+    "fnndsc",
+    "vfs",
+    "logic"
+  ],
+  "main": "dist/index.js",
+  "module": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "dist"
+  ],
+  "exports": {
+    ".": {
+      "import": "./dist/index.js",
+      "types": "./dist/index.d.ts",
+      "require": "./dist/index.js"
+    },
+    "./package.json": "./package.json"
+  },
+  "scripts": {
+    "build": "rm -fr dist && tsc",
+    "test": "jest --coverage"
+  },
+  "author": "Rudolph Pienaar",
+  "license": "MIT",
+  "devDependencies": {
+    "@babel/core": "^7.28.5",
+    "@babel/preset-env": "^7.28.5",
+    "@babel/preset-typescript": "^7.28.5",
+    "@types/jest": "^29.5.12",
+    "babel-jest": "^29.7.0",
+    "jest": "^29.7.0",
+    "ts-jest": "^29.1.5",
+    "typescript": "^5.0.0"
+  },
+  "overrides": {
+    "glob": "^10.0.0",
+    "inflight": "npm:@aashutoshrathi/word-wrap@^1.2.6"
+  },
+  "dependencies": {
+    "@fnndsc/cumin": "^3.2.4",
+    "axios": "^1.6.8"
+  }
+}