@fnndsc/salsa 3.5.1 → 3.6.1

package/dist/index.js

@@ -18,7 +18,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.feedGraphData_ensure = exports.nodeJoins_resolve = exports.feedJoins_ensure = exports.signature_compute = exports.feedGraph_build = exports.feedStatus_refresh = exports.feedMeta_ensure = exports.feedInstances_ensureLoaded = exports.procFeed_ensureLoaded = exports.procTopology_await = exports.procTopology_status = exports.procTopology_warmup = exports.procCache_refresh = void 0;
+exports.feedGraphData_ensure = exports.nodeJoins_resolve = exports.feedJoins_ensure = exports.signature_compute = exports.feedGraph_build = exports.feedStatus_refresh = exports.feedMeta_ensure = exports.feedInstances_ensureLoaded = exports.procFeed_ensureLoaded = exports.procTopology_await = exports.procTopology_status = exports.procTopology_retry = exports.procTopology_reconcileFeeds = exports.procTopology_warmup = exports.procCache_refresh = void 0;
 __exportStar(require("./feeds/index.js"), exports);
 __exportStar(require("./plugins/index.js"), exports);
 __exportStar(require("./files/index.js"), exports);
@@ -27,6 +27,7 @@ __exportStar(require("./context/index.js"), exports);
 __exportStar(require("./store/index.js"), exports);
 __exportStar(require("./pipelines/index.js"), exports);
 __exportStar(require("./pacs/index.js"), exports);
+__exportStar(require("./retrieve/watch.js"), exports);
 __exportStar(require("./vfs/index.js"), exports);
 __exportStar(require("./tags/index.js"), exports);
 __exportStar(require("./groups/index.js"), exports);
@@ -35,9 +36,12 @@ __exportStar(require("./plugininstances/index.js"), exports);
 __exportStar(require("./workflows/index.js"), exports);
 __exportStar(require("./compute/index.js"), exports);
 __exportStar(require("./jobs/index.js"), exports);
+__exportStar(require("./users/index.js"), exports);
 var proc_js_1 = require("./vfs/providers/proc.js");
 Object.defineProperty(exports, "procCache_refresh", { enumerable: true, get: function () { return proc_js_1.procCache_refresh; } });
 Object.defineProperty(exports, "procTopology_warmup", { enumerable: true, get: function () { return proc_js_1.procTopology_warmup; } });
+Object.defineProperty(exports, "procTopology_reconcileFeeds", { enumerable: true, get: function () { return proc_js_1.procTopology_reconcileFeeds; } });
+Object.defineProperty(exports, "procTopology_retry", { enumerable: true, get: function () { return proc_js_1.procTopology_retry; } });
 Object.defineProperty(exports, "procTopology_status", { enumerable: true, get: function () { return proc_js_1.procTopology_status; } });
 Object.defineProperty(exports, "procTopology_await", { enumerable: true, get: function () { return proc_js_1.procTopology_await; } });
 Object.defineProperty(exports, "procFeed_ensureLoaded", { enumerable: true, get: function () { return proc_js_1.procFeed_ensureLoaded; } });

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAAA;;;GAGG;;;;;;;;;;;;;;;;;AAEH,mDAAiC;AACjC,qDAAmC;AACnC,mDAAiC;AACjC,qDAAmC;AACnC,qDAAmC;AACnC,mDAAiC;AACjC,uDAAqC;AACrC,kDAAgC;AAChC,iDAA+B;AAC/B,kDAAgC;AAChC,oDAAkC;AAClC,yDAAuC;AACvC,6DAA2C;AAC3C,uDAAqC;AACrC,qDAAmC;AACnC,kDAAgC;AAChC,mDAAkN;AAAzM,4GAAA,iBAAiB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,gHAAA,qBAAqB,OAAA;AAAE,qHAAA,0BAA0B,OAAA;AAAE,0GAAA,eAAe,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAEhL,mDAAwE;AAA/D,+GAAA,eAAe,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAE3C,mDAAyE;AAAhE,gHAAA,gBAAgB,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAC5C,iDAAyD;AAAhD,mHAAA,oBAAoB,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAAA;;;GAGG;;;;;;;;;;;;;;;;;AAEH,mDAAiC;AACjC,qDAAmC;AACnC,mDAAiC;AACjC,qDAAmC;AACnC,qDAAmC;AACnC,mDAAiC;AACjC,uDAAqC;AACrC,kDAAgC;AAChC,sDAAoC;AACpC,iDAA+B;AAC/B,kDAAgC;AAChC,oDAAkC;AAClC,yDAAuC;AACvC,6DAA2C;AAC3C,uDAAqC;AACrC,qDAAmC;AACnC,kDAAgC;AAChC,mDAAiC;AACjC,mDAAmQ;AAA1P,4GAAA,iBAAiB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,gHAAA,qBAAqB,OAAA;AAAE,qHAAA,0BAA0B,OAAA;AAAE,0GAAA,eAAe,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAEjO,mDAAwE;AAA/D,+GAAA,eAAe,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAE3C,mDAAyE;AAAhE,gHAAA,gBAAgB,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAC5C,iDAAyD;AAAhD,mHAAA,oBAAoB,OAAA"}

package/dist/jobs/jobOps.d.ts

@@ -1,6 +1,10 @@
 /**
  * @file Job (plugin instance) cancel and delete operations.
  *
+ * All CUBE access flows through cumin's typed wire contract
+ * (`pluginInstance_get`, `pluginInstancesPage_get`) — no casts against the
+ * opaque client belong here.
+ *
  * @module
  */
 import { Result } from '@fnndsc/cumin';
@@ -45,15 +49,6 @@ export declare function job_delete(instanceID: number): Promise<Result<boolean>>
  * ```
  */
 export declare function job_statusFetch(instanceID: number): Promise<Result<string>>;
-/**
- * Finds plugin instances by numeric ID or plugin name substring.
- *
- * Checks ProcCache first. On a miss, queries the API and loads the
- * relevant feed(s) into the cache so paths can be reconstructed.
- *
- * @param term - Numeric instance ID string, or plugin name substring.
- * @returns Ok(array of {id, feedID, pluginName, status}) or Err.
- *
 /**
  * Fetches current status for a batch of plugin instances in parallel.
  * Used by ls -l /proc/jobs/feed_N to get all node statuses in one round-trip.

package/dist/jobs/jobOps.js

@@ -2,6 +2,10 @@
 /**
  * @file Job (plugin instance) cancel and delete operations.
  *
+ * All CUBE access flows through cumin's typed wire contract
+ * (`pluginInstance_get`, `pluginInstancesPage_get`) — no casts against the
+ * opaque client belong here.
+ *
  * @module
  */
 Object.defineProperty(exports, "__esModule", { value: true });
@@ -13,12 +17,38 @@ exports.jobs_find = jobs_find;
 exports.job_feedID_get = job_feedID_get;
 exports.job_logFetch = job_logFetch;
 const cumin_1 = require("@fnndsc/cumin");
+const node_zlib_1 = require("node:zlib");
 /** Statuses that cannot be cancelled — operation is already done. */
 const TERMINAL_STATUSES = new Set([
     'finishedSuccessfully',
     'finishedWithError',
     'cancelled',
 ]);
+/** Tests whether an unknown value is a non-null record. */
+function record_is(value) {
+    return typeof value === 'object' && value !== null;
+}
+/**
+ * Decodes CUBE's base64-encoded, zlib-compressed raw pfcon response and
+ * extracts its complete compute log.
+ *
+ * @param raw - The `PluginInstance.raw` value returned by CUBE.
+ * @returns The complete compute log, or undefined when no decodable log exists.
+ */
+function pfconLog_decode(raw) {
+    if (typeof raw !== 'string' || raw.length === 0)
+        return undefined;
+    try {
+        const json = JSON.parse((0, node_zlib_1.inflateSync)(Buffer.from(raw, 'base64')).toString('utf8'));
+        if (!record_is(json) || !record_is(json['compute']))
+            return undefined;
+        const logs = json['compute']['logs'];
+        return typeof logs === 'string' ? logs : undefined;
+    }
+    catch {
+        return undefined;
+    }
+}
 /**
  * Cancels a running or scheduled plugin instance.
  * No-op if already terminal (returns Ok).
@@ -39,16 +69,16 @@ async function job_cancel(instanceID) {
             cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
             return (0, cumin_1.Err)();
         }
-        const instance = await client.getPluginInstance(instanceID);
-        if (!instance) {
+        const handle = await (0, cumin_1.pluginInstance_get)(client, instanceID);
+        if (!handle) {
             cumin_1.errorStack.stack_push('error', `Plugin instance ${instanceID} not found.`);
             return (0, cumin_1.Err)();
         }
-        const status = instance.data.status ?? '';
+        const status = handle.data?.status ?? '';
         if (TERMINAL_STATUSES.has(status)) {
             return (0, cumin_1.Ok)(true);
         }
-        await instance.put({ status: 'cancelled' });
+        await handle.status_set('cancelled');
         return (0, cumin_1.Ok)(true);
     }
     catch (error) {
@@ -77,16 +107,16 @@ async function job_delete(instanceID) {
             cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
             return (0, cumin_1.Err)();
         }
-        const instance = await client.getPluginInstance(instanceID);
-        if (!instance) {
+        const handle = await (0, cumin_1.pluginInstance_get)(client, instanceID);
+        if (!handle) {
             cumin_1.errorStack.stack_push('error', `Plugin instance ${instanceID} not found.`);
             return (0, cumin_1.Err)();
         }
-        const status = instance.data.status ?? '';
+        const status = handle.data?.status ?? '';
         if (!TERMINAL_STATUSES.has(status)) {
-            await instance.put({ status: 'cancelled' });
+            await handle.status_set('cancelled');
         }
-        await instance.delete();
+        await handle.delete();
         return (0, cumin_1.Ok)(true);
     }
     catch (error) {
@@ -114,13 +144,12 @@ async function job_statusFetch(instanceID) {
             cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
             return (0, cumin_1.Err)();
         }
-        const instance = await client.getPluginInstance(instanceID);
-        if (!instance) {
+        const handle = await (0, cumin_1.pluginInstance_get)(client, instanceID);
+        if (!handle) {
             cumin_1.errorStack.stack_push('error', `Plugin instance ${instanceID} not found.`);
             return (0, cumin_1.Err)();
         }
-        const status = instance.data.status ?? 'unknown';
-        return (0, cumin_1.Ok)(status);
+        return (0, cumin_1.Ok)(handle.data?.status ?? 'unknown');
     }
     catch (error) {
         const msg = error instanceof Error ? error.message : String(error);
@@ -128,15 +157,6 @@ async function job_statusFetch(instanceID) {
         return (0, cumin_1.Err)();
     }
 }
-/**
- * Finds plugin instances by numeric ID or plugin name substring.
- *
- * Checks ProcCache first. On a miss, queries the API and loads the
- * relevant feed(s) into the cache so paths can be reconstructed.
- *
- * @param term - Numeric instance ID string, or plugin name substring.
- * @returns Ok(array of {id, feedID, pluginName, status}) or Err.
- *
 /**
  * Fetches current status for a batch of plugin instances in parallel.
  * Used by ls -l /proc/jobs/feed_N to get all node statuses in one round-trip.
@@ -155,21 +175,32 @@ async function jobs_statusBatch(ids) {
     if (ids.length === 0)
         return result;
     const client = await cumin_1.chrisConnection.client_get();
-    if (!client)
+    if (!client) {
+        // An empty map from a disconnected client is not "no jobs": say so, so
+        // callers rendering stale status have a visible reason.
+        cumin_1.errorStack.stack_push("warning", `jobs_statusBatch: not connected; status for ${ids.length} instance(s) unavailable.`);
         return result;
-    const typedClient = client;
+    }
+    const failedIDs = [];
     const entries = (await Promise.all(ids.map(async (id) => {
         try {
-            const inst = await typedClient.getPluginInstance(id);
-            if (!inst)
+            const handle = await (0, cumin_1.pluginInstance_get)(client, id);
+            if (!handle) {
+                failedIDs.push(id);
                 return null;
-            const status = inst.data.status ?? 'unknown';
-            return [id, status];
+            }
+            return [id, handle.data?.status ?? 'unknown'];
         }
         catch {
+            failedIDs.push(id);
             return null;
         }
     }))).filter((e) => e !== null);
+    // Partial results are by design (one dead instance must not blank a whole
+    // listing), but the gaps must be visible rather than reading as absent.
+    if (failedIDs.length > 0) {
+        cumin_1.errorStack.stack_push("warning", `jobs_statusBatch: could not fetch status for instance(s) ${failedIDs.sort((a, b) => a - b).join(", ")}.`);
+    }
     for (const [id, status] of entries) {
         result.set(id, status);
     }
@@ -217,8 +248,11 @@ async function jobs_find(term) {
         const apiResults = [];
         let offset = 0;
         while (true) {
-            const page = await client.getPluginInstances({ ...searchParam, offset });
-            const chunk = page.data ?? [];
+            const page = await (0, cumin_1.pluginInstancesPage_get)(client, {
+                ...searchParam,
+                offset,
+            });
+            const chunk = page.data;
             for (const inst of chunk) {
                 apiResults.push({
                     id: Number(inst.id),
@@ -257,8 +291,11 @@ async function job_feedID_get(instanceID) {
             cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
             return (0, cumin_1.Err)();
         }
-        const result = await client.getPluginInstances({ id: instanceID, limit: 1 });
-        const hit = result.data?.[0];
+        const page = await (0, cumin_1.pluginInstancesPage_get)(client, {
+            id: instanceID,
+            limit: 1,
+        });
+        const hit = page.data[0];
         if (!hit || hit.feed_id === undefined || hit.feed_id === null) {
             cumin_1.errorStack.stack_push('error', `Instance ${instanceID} not found.`);
             return (0, cumin_1.Err)();
@@ -284,18 +321,19 @@ async function job_logFetch(instanceID) {
             cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
             return (0, cumin_1.Err)();
         }
-        const instance = await client.getPluginInstance(instanceID);
-        if (!instance) {
+        const handle = await (0, cumin_1.pluginInstance_get)(client, instanceID);
+        if (!handle) {
             cumin_1.errorStack.stack_push('error', `Plugin instance ${instanceID} not found.`);
             return (0, cumin_1.Err)();
         }
-        if (!instance.getLogs) {
+        const rawLog = pfconLog_decode(handle.data?.raw);
+        if (rawLog !== undefined) {
+            return (0, cumin_1.Ok)(rawLog || '(no log output yet)');
+        }
+        const logText = await handle.logs_get();
+        if (logText === null) {
             return (0, cumin_1.Ok)('(log not available for this instance)');
         }
-        const logsResult = await instance.getLogs();
-        const logText = logsResult.data
-            .map((entry) => entry.log ?? '')
-            .join('\n');
         return (0, cumin_1.Ok)(logText || '(no log output yet)');
     }
     catch (error) {

package/dist/jobs/jobOps.js.map

@@ -1 +1 @@
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package/dist/pipelines/diagram.js

@@ -11,6 +11,17 @@ exports.pipelineDiagram_get = pipelineDiagram_get;
  * @module
  */
 const cumin_1 = require("@fnndsc/cumin");
+/**
+ * Narrows a wire default-parameter row to the diagram's required shape.
+ *
+ * @param row - Stored default row from the contract.
+ * @returns The narrowed row, or null when required fields are absent.
+ */
+function defaultParameter_narrow(row) {
+    if (typeof row.plugin_piping_id !== 'number' || typeof row.param_name !== 'string')
+        return null;
+    return { plugin_piping_id: row.plugin_piping_id, param_name: row.param_name, value: row.value };
+}
 /**
  * Parses the additional parents stored in a `plugininstances` default.
  *
@@ -42,20 +53,19 @@ async function pipelineDiagram_get(specifier) {
         return (0, cumin_1.Err)();
     }
     try {
-        const pipeline = await client.getPipeline(resolved.value.id);
+        const pipeline = await (0, cumin_1.pipeline_get)(client, resolved.value.id);
         if (!pipeline) {
             cumin_1.errorStack.stack_push('error', `Pipeline ${resolved.value.id} not found.`);
             return (0, cumin_1.Err)();
         }
-        const collections = await Promise.all([
-            pipeline.getPluginPipings({ limit: 1000 }),
-            pipeline.getDefaultParameters({ limit: 1000 }),
+        const [pipingItems, defaultsPage] = await Promise.all([
+            pipeline.pluginPipings_get({ limit: 1000 }),
+            pipeline.defaultParametersPage_get({ limit: 1000 }),
         ]);
-        const pipingList = collections[0];
-        const defaultList = collections[1];
-        const pipings = (0, cumin_1.items_get)(pipingList)
-            .map((item) => item.data);
-        const defaults = (0, cumin_1.listData_get)(defaultList);
+        const pipings = pipingItems.map((item) => item.data);
+        const defaults = defaultsPage.data
+            .map((row) => defaultParameter_narrow(row))
+            .filter((row) => row !== null);
         const defaultsByPiping = new Map();
         const joinsByPiping = new Map();
         for (const parameter of defaults) {

package/dist/pipelines/diagram.js.map

@@ -1 +1 @@
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package/dist/pipelines/index.d.ts

@@ -8,6 +8,10 @@
  */
 import { FilteredResourceData, ListOptions, Result, PipelineRecord, WorkflowResult } from '@fnndsc/cumin';
 export { pipelineDiagram_get, type PipelineDiagram, type PipelineDiagramArgument, type PipelineDiagramNode, } from './diagram.js';
+export { pipelineManifest_get, type PipelineManifest, type PipelineManifestGetOptions, type PipelineManifestNode, type PipelineManifestParameterDefault, } from './manifest.js';
+export { pipelineInvocation_prepare, type PipelineInvocationBinding, type PipelineInvocationPrepareOptions, type PipelineParameterDefinition, type PreparedPipelineInvocation, type PreparedWorkflowNode, } from './invocation.js';
+import { type PipelineManifest } from './manifest.js';
+import { type PipelineInvocationBinding } from './invocation.js';
 export type { PipelineRecord, WorkflowResult };
 /**
  * Lists registered pipelines, optionally filtered by name substring.
@@ -35,14 +39,33 @@ export declare function pipelineFields_get(): Promise<string[] | null>;
  */
 export declare function pipelines_getAll(): Promise<Result<PipelineRecord[]>>;
 /**
- * Runs a pipeline by name or ID, attaching it to a previous plugin instance.
+ * Project one exact Pipeline executable slug without listing every Pipeline.
+ *
+ * The stable `_id<N>` suffix identifies the candidate Pipeline. The targeted
+ * source-file lookup then verifies the complete slug before it is accepted.
+ *
+ * @param slug - Exact Pipeline basename exposed in `/bin`.
+ * @returns The registered invocation manifest for the exact Pipeline slug.
+ */
+export declare function pipelineManifestBySlug_get(slug: string): Promise<Result<PipelineManifest>>;
+/** Runtime overlays accepted by `pipeline_run`. */
+export interface PipelineRunOptions {
+    /** Compute placement baseline applied before node-specific overlays. */
+    globalCompute?: string;
+    /** Parsed sparse or complete registered-manifest YAML overlay. */
+    parameterFile?: unknown;
+    /** Explicit node-qualified values, with highest precedence. */
+    cliBindings?: PipelineInvocationBinding[];
+}
+/**
+ * Run a pipeline by name or ID, attaching it to a previous plugin instance.
  *
  * @param nameOrId - Pipeline name or numeric ID string.
- * @param previousPluginInstId - The plugin instance to attach the pipeline root to.
- * @param computeOverride - Optional compute resource name applied to all nodes.
- * @returns Result containing workflow ID and created plugin instance IDs.
+ * @param previousPluginInstId - Plugin instance to which pipeline roots attach.
+ * @param invocationOptions - Runtime overlays, or the legacy global compute string.
+ * @returns Result containing Workflow ID and created plugin instance IDs.
  */
-export declare function pipeline_run(nameOrId: string, previousPluginInstId: number, computeOverride?: string): Promise<Result<WorkflowResult>>;
+export declare function pipeline_run(nameOrId: string, previousPluginInstId: number, invocationOptions?: PipelineRunOptions | string): Promise<Result<WorkflowResult>>;
 /**
  * Fetches the YAML source of a registered pipeline by searching /PIPELINES/ for
  * a file whose basename matches the pipeline name.