@fnndsc/salsa 3.2.4

package/dist/jobs/jobOps.d.ts

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+/**
+ * @file Job (plugin instance) cancel and delete operations.
+ *
+ * @module
+ */
+import { Result } from '@fnndsc/cumin';
+/**
+ * Cancels a running or scheduled plugin instance.
+ * No-op if already terminal (returns Ok).
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(true) on success, Err on failure.
+ *
+ * @example
+ * ```typescript
+ * const result = await job_cancel(789);
+ * if (!result.ok) console.error('Cancel failed');
+ * ```
+ */
+export declare function job_cancel(instanceID: number): Promise<Result<boolean>>;
+/**
+ * Deletes a plugin instance record from ChRIS.
+ * Only call on terminal instances — cancels first if non-terminal.
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(true) on success, Err on failure.
+ *
+ * @example
+ * ```typescript
+ * const result = await job_delete(789);
+ * if (!result.ok) console.error('Delete failed');
+ * ```
+ */
+export declare function job_delete(instanceID: number): Promise<Result<boolean>>;
+/**
+ * Fetches the current status string for a plugin instance directly from the API.
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(statusString) or Err on failure.
+ *
+ * @example
+ * ```typescript
+ * const result = await job_statusFetch(789);
+ * if (result.ok) console.log(result.value); // 'finishedSuccessfully'
+ * ```
+ */
+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.
+ *
+ * @param ids - Array of instance IDs.
+ * @returns Map from instance ID to status string. Missing entries on failure.
+ *
+ * @example
+ * ```typescript
+ * const statuses = await jobs_statusBatch([456, 789, 1011]);
+ * statuses.get(789); // 'finishedSuccessfully'
+ * ```
+ */
+export declare function jobs_statusBatch(ids: number[]): Promise<Map<number, string>>;
+/**
+ * Finds plugin instances by numeric ID or plugin name substring.
+ * After warm-up completes uses pure in-memory cache; otherwise falls back to API.
+ *
+ * @param term - Numeric instance ID or plugin name substring.
+ * @returns Ok(array of matches) or Err.
+ *
+ * @example
+ * ```typescript
+ * await jobs_find('64306');     // exact ID
+ * await jobs_find('pl-fshack'); // all instances whose name contains 'pl-fshack'
+ * ```
+ */
+export declare function jobs_find(term: string): Promise<Result<Array<{
+    id: number;
+    feedID: number;
+    pluginName: string;
+}>>>;
+/**
+ * Looks up which feed a plugin instance belongs to.
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(feedID) or Err if not found.
+ *
+ * @example
+ * ```typescript
+ * const r = await job_feedID_get(64306);
+ * if (r.ok) console.log(r.value); // 1107
+ * ```
+ */
+export declare function job_feedID_get(instanceID: number): Promise<Result<number>>;
+/**
+ * Fetches the log output for a plugin instance from the API.
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(logString) or Err on failure.
+ */
+export declare function job_logFetch(instanceID: number): Promise<Result<string>>;

package/dist/jobs/jobOps.js

@@ -0,0 +1,307 @@
+"use strict";
+/**
+ * @file Job (plugin instance) cancel and delete operations.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.job_cancel = job_cancel;
+exports.job_delete = job_delete;
+exports.job_statusFetch = job_statusFetch;
+exports.jobs_statusBatch = jobs_statusBatch;
+exports.jobs_find = jobs_find;
+exports.job_feedID_get = job_feedID_get;
+exports.job_logFetch = job_logFetch;
+const cumin_1 = require("@fnndsc/cumin");
+/** Statuses that cannot be cancelled — operation is already done. */
+const TERMINAL_STATUSES = new Set([
+    'finishedSuccessfully',
+    'finishedWithError',
+    'cancelled',
+]);
+/**
+ * Cancels a running or scheduled plugin instance.
+ * No-op if already terminal (returns Ok).
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(true) on success, Err on failure.
+ *
+ * @example
+ * ```typescript
+ * const result = await job_cancel(789);
+ * if (!result.ok) console.error('Cancel failed');
+ * ```
+ */
+async function job_cancel(instanceID) {
+    try {
+        const client = await cumin_1.chrisConnection.client_get();
+        if (!client) {
+            cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
+            return (0, cumin_1.Err)();
+        }
+        const instance = await client.getPluginInstance(instanceID);
+        if (!instance) {
+            cumin_1.errorStack.stack_push('error', `Plugin instance ${instanceID} not found.`);
+            return (0, cumin_1.Err)();
+        }
+        const status = instance.data.status ?? '';
+        if (TERMINAL_STATUSES.has(status)) {
+            return (0, cumin_1.Ok)(true);
+        }
+        await instance.put({ status: 'cancelled' });
+        return (0, cumin_1.Ok)(true);
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push('error', `Failed to cancel instance ${instanceID}: ${msg}`);
+        return (0, cumin_1.Err)();
+    }
+}
+/**
+ * Deletes a plugin instance record from ChRIS.
+ * Only call on terminal instances — cancels first if non-terminal.
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(true) on success, Err on failure.
+ *
+ * @example
+ * ```typescript
+ * const result = await job_delete(789);
+ * if (!result.ok) console.error('Delete failed');
+ * ```
+ */
+async function job_delete(instanceID) {
+    try {
+        const client = await cumin_1.chrisConnection.client_get();
+        if (!client) {
+            cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
+            return (0, cumin_1.Err)();
+        }
+        const instance = await client.getPluginInstance(instanceID);
+        if (!instance) {
+            cumin_1.errorStack.stack_push('error', `Plugin instance ${instanceID} not found.`);
+            return (0, cumin_1.Err)();
+        }
+        const status = instance.data.status ?? '';
+        if (!TERMINAL_STATUSES.has(status)) {
+            await instance.put({ status: 'cancelled' });
+        }
+        await instance.delete();
+        return (0, cumin_1.Ok)(true);
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push('error', `Failed to delete instance ${instanceID}: ${msg}`);
+        return (0, cumin_1.Err)();
+    }
+}
+/**
+ * Fetches the current status string for a plugin instance directly from the API.
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(statusString) or Err on failure.
+ *
+ * @example
+ * ```typescript
+ * const result = await job_statusFetch(789);
+ * if (result.ok) console.log(result.value); // 'finishedSuccessfully'
+ * ```
+ */
+async function job_statusFetch(instanceID) {
+    try {
+        const client = await cumin_1.chrisConnection.client_get();
+        if (!client) {
+            cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
+            return (0, cumin_1.Err)();
+        }
+        const instance = await client.getPluginInstance(instanceID);
+        if (!instance) {
+            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);
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push('error', `Failed to fetch status for instance ${instanceID}: ${msg}`);
+        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.
+ *
+ * @param ids - Array of instance IDs.
+ * @returns Map from instance ID to status string. Missing entries on failure.
+ *
+ * @example
+ * ```typescript
+ * const statuses = await jobs_statusBatch([456, 789, 1011]);
+ * statuses.get(789); // 'finishedSuccessfully'
+ * ```
+ */
+async function jobs_statusBatch(ids) {
+    const result = new Map();
+    if (ids.length === 0)
+        return result;
+    const client = await cumin_1.chrisConnection.client_get();
+    if (!client)
+        return result;
+    const typedClient = client;
+    const entries = (await Promise.all(ids.map(async (id) => {
+        try {
+            const inst = await typedClient.getPluginInstance(id);
+            if (!inst)
+                return null;
+            const status = inst.data.status ?? 'unknown';
+            return [id, status];
+        }
+        catch {
+            return null;
+        }
+    }))).filter((e) => e !== null);
+    for (const [id, status] of entries) {
+        result.set(id, status);
+    }
+    return result;
+}
+/**
+ * Finds plugin instances by numeric ID or plugin name substring.
+ * After warm-up completes uses pure in-memory cache; otherwise falls back to API.
+ *
+ * @param term - Numeric instance ID or plugin name substring.
+ * @returns Ok(array of matches) or Err.
+ *
+ * @example
+ * ```typescript
+ * await jobs_find('64306');     // exact ID
+ * await jobs_find('pl-fshack'); // all instances whose name contains 'pl-fshack'
+ * ```
+ */
+async function jobs_find(term) {
+    try {
+        const cache = (0, cumin_1.procCache_get)();
+        const numeric = parseInt(term, 10);
+        const isID = !isNaN(numeric) && String(numeric) === term;
+        // After warm-up: topology is complete — pure in-memory, zero API calls.
+        if (cache.warmupComplete) {
+            const hits = cache.instances_find(term);
+            return (0, cumin_1.Ok)(hits.map(i => ({ id: i.id, feedID: i.feedID, pluginName: i.pluginName })));
+        }
+        // Exact ID: cache-first (only one possible result when warm-up is partial)
+        if (isID) {
+            const cached = cache.instances_find(term);
+            if (cached.length > 0) {
+                return (0, cumin_1.Ok)(cached.map(i => ({ id: i.id, feedID: i.feedID, pluginName: i.pluginName })));
+            }
+        }
+        // Name substring or ID miss: fall back to API during warm-up
+        const client = await cumin_1.chrisConnection.client_get();
+        if (!client) {
+            cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
+            return (0, cumin_1.Err)();
+        }
+        const searchParam = isID
+            ? { id: numeric, limit: 1, offset: 0 }
+            : { plugin_name: term, limit: 100, offset: 0 };
+        const apiResults = [];
+        let offset = 0;
+        while (true) {
+            const page = await client.getPluginInstances({ ...searchParam, offset });
+            const chunk = page.data ?? [];
+            for (const inst of chunk) {
+                apiResults.push({
+                    id: Number(inst.id),
+                    feedID: Number(inst.feed_id),
+                    pluginName: String(inst.plugin_name),
+                });
+            }
+            if (isID || chunk.length < 100)
+                break;
+            offset += 100;
+        }
+        return (0, cumin_1.Ok)(apiResults);
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push('error', `jobs_find failed: ${msg}`);
+        return (0, cumin_1.Err)();
+    }
+}
+/**
+ * Looks up which feed a plugin instance belongs to.
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(feedID) or Err if not found.
+ *
+ * @example
+ * ```typescript
+ * const r = await job_feedID_get(64306);
+ * if (r.ok) console.log(r.value); // 1107
+ * ```
+ */
+async function job_feedID_get(instanceID) {
+    try {
+        const client = await cumin_1.chrisConnection.client_get();
+        if (!client) {
+            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];
+        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)();
+        }
+        return (0, cumin_1.Ok)(Number(hit.feed_id));
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push('error', `Failed to find feed for instance ${instanceID}: ${msg}`);
+        return (0, cumin_1.Err)();
+    }
+}
+/**
+ * Fetches the log output for a plugin instance from the API.
+ *
+ * @param instanceID - The plugin instance ID.
+ * @returns Ok(logString) or Err on failure.
+ */
+async function job_logFetch(instanceID) {
+    try {
+        const client = await cumin_1.chrisConnection.client_get();
+        if (!client) {
+            cumin_1.errorStack.stack_push('error', 'Not connected to ChRIS.');
+            return (0, cumin_1.Err)();
+        }
+        const instance = await client.getPluginInstance(instanceID);
+        if (!instance) {
+            cumin_1.errorStack.stack_push('error', `Plugin instance ${instanceID} not found.`);
+            return (0, cumin_1.Err)();
+        }
+        if (!instance.getLogs) {
+            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) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push('error', `Failed to fetch log for instance ${instanceID}: ${msg}`);
+        return (0, cumin_1.Err)();
+    }
+}
+//# sourceMappingURL=jobOps.js.map

package/dist/jobs/jobOps.js.map

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

@@ -0,0 +1,64 @@
+/**
+ * @file PACS operations.
+ * @module
+ */
+import { PACSServer, PACSServerListOptions, PACSQueryListOptions, PACSQueryCreateData, PACSRetrieveRecord, PACSQueryStatusReport, Result, FilteredResourceData, PACSQueryRecord, PACSQueryDecodedResult, ListOptions } from "@fnndsc/cumin";
+/**
+ * List PACS servers from the connected CUBE.
+ *
+ * @param options - Optional identifier/limit/offset filters.
+ * @returns Result containing PACS servers or Err on failure.
+ */
+export declare function pacsServers_list(options?: PACSServerListOptions): Promise<Result<PACSServer[]>>;
+/**
+ * List PACS queries.
+ *
+ * @param options - Optional filters (pacs_id, pacs_identifier, limit, offset).
+ * @returns Result containing FilteredResourceData or null.
+ */
+export declare function pacsQueries_list(options?: PACSQueryListOptions): Promise<Result<FilteredResourceData | null>>;
+/**
+ * Create a PACS query against a PACS server.
+ *
+ * @param pacsserver - PACS server ID or identifier.
+ * @param data - Query creation data.
+ * @returns Result containing PACSQueryRecord.
+ */
+export declare function pacsQueries_create(pacsserver: string, data: PACSQueryCreateData): Promise<Result<PACSQueryRecord>>;
+/**
+ * Decode the result payload of a PACS query.
+ *
+ * @param queryId - PACS query ID.
+ * @returns Result containing decoded payload forms.
+ */
+export declare function pacsQuery_resultDecode(queryId: number): Promise<Result<PACSQueryDecodedResult>>;
+/**
+ * Create a PACS retrieve to pull DICOM data from PACS to ChRIS.
+ *
+ * @param queryId - PACS query ID to retrieve data for.
+ * @returns Result containing PACSRetrieveRecord.
+ */
+export declare function pacsRetrieve_create(queryId: number): Promise<Result<PACSRetrieveRecord>>;
+/**
+ * List all retrieves for a given PACS query.
+ *
+ * @param queryId - PACS query ID.
+ * @param options - Optional list options.
+ * @returns Result containing array of PACSRetrieveRecord.
+ */
+export declare function pacsRetrieves_list(queryId: number, options?: ListOptions): Promise<Result<PACSRetrieveRecord[]>>;
+/**
+ * Delete (cancel) a PACS retrieve.
+ *
+ * @param retrieveId - PACS retrieve ID to delete.
+ * @returns Result containing void.
+ */
+export declare function pacsRetrieve_delete(retrieveId: number): Promise<Result<void>>;
+/**
+ * Generate a complete status report for a PACS query retrieve.
+ * Combines query decode results with actual file counts to show progress.
+ *
+ * @param queryId - PACS query ID.
+ * @returns Result containing PACSQueryStatusReport with series-level status.
+ */
+export declare function pacsRetrieve_statusForQuery(queryId: number): Promise<Result<PACSQueryStatusReport>>;

package/dist/pacs/index.js

@@ -0,0 +1,91 @@
+"use strict";
+/**
+ * @file PACS operations.
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pacsServers_list = pacsServers_list;
+exports.pacsQueries_list = pacsQueries_list;
+exports.pacsQueries_create = pacsQueries_create;
+exports.pacsQuery_resultDecode = pacsQuery_resultDecode;
+exports.pacsRetrieve_create = pacsRetrieve_create;
+exports.pacsRetrieves_list = pacsRetrieves_list;
+exports.pacsRetrieve_delete = pacsRetrieve_delete;
+exports.pacsRetrieve_statusForQuery = pacsRetrieve_statusForQuery;
+const cumin_1 = require("@fnndsc/cumin");
+/**
+ * List PACS servers from the connected CUBE.
+ *
+ * @param options - Optional identifier/limit/offset filters.
+ * @returns Result containing PACS servers or Err on failure.
+ */
+async function pacsServers_list(options = {}) {
+    return (0, cumin_1.pacsServers_list)(options);
+}
+/**
+ * List PACS queries.
+ *
+ * @param options - Optional filters (pacs_id, pacs_identifier, limit, offset).
+ * @returns Result containing FilteredResourceData or null.
+ */
+async function pacsQueries_list(options = {}) {
+    return (0, cumin_1.pacsQueries_list)(options);
+}
+/**
+ * Create a PACS query against a PACS server.
+ *
+ * @param pacsserver - PACS server ID or identifier.
+ * @param data - Query creation data.
+ * @returns Result containing PACSQueryRecord.
+ */
+async function pacsQueries_create(pacsserver, data) {
+    return (0, cumin_1.pacsQueries_create)(pacsserver, data);
+}
+/**
+ * Decode the result payload of a PACS query.
+ *
+ * @param queryId - PACS query ID.
+ * @returns Result containing decoded payload forms.
+ */
+async function pacsQuery_resultDecode(queryId) {
+    return (0, cumin_1.pacsQuery_resultDecode)(queryId);
+}
+/**
+ * Create a PACS retrieve to pull DICOM data from PACS to ChRIS.
+ *
+ * @param queryId - PACS query ID to retrieve data for.
+ * @returns Result containing PACSRetrieveRecord.
+ */
+async function pacsRetrieve_create(queryId) {
+    return (0, cumin_1.pacsRetrieve_create)(queryId);
+}
+/**
+ * List all retrieves for a given PACS query.
+ *
+ * @param queryId - PACS query ID.
+ * @param options - Optional list options.
+ * @returns Result containing array of PACSRetrieveRecord.
+ */
+async function pacsRetrieves_list(queryId, options) {
+    return (0, cumin_1.pacsRetrieves_list)(queryId, options);
+}
+/**
+ * Delete (cancel) a PACS retrieve.
+ *
+ * @param retrieveId - PACS retrieve ID to delete.
+ * @returns Result containing void.
+ */
+async function pacsRetrieve_delete(retrieveId) {
+    return (0, cumin_1.pacsRetrieve_delete)(retrieveId);
+}
+/**
+ * Generate a complete status report for a PACS query retrieve.
+ * Combines query decode results with actual file counts to show progress.
+ *
+ * @param queryId - PACS query ID.
+ * @returns Result containing PACSQueryStatusReport with series-level status.
+ */
+async function pacsRetrieve_statusForQuery(queryId) {
+    return (0, cumin_1.pacsRetrieve_statusForQuery)(queryId);
+}
+//# sourceMappingURL=index.js.map

package/dist/pacs/index.js.map

@@ -0,0 +1 @@
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package/dist/pacs/resultDecode.d.ts

@@ -0,0 +1,13 @@
+/**
+ * @file Thin salsa wrapper around cumin's PACS query result decoder.
+ *
+ * @module
+ */
+import { PACSQueryDecodedResult, Result } from "@fnndsc/cumin";
+/**
+ * Decode the result payload of a PACS query by ID.
+ *
+ * @param queryId - PACS query ID.
+ * @returns Result containing decoded payload (raw, decoded buffers/text/json) or Err.
+ */
+export declare function pacsQuery_resultDecode(queryId: number): Promise<Result<PACSQueryDecodedResult>>;

package/dist/pacs/resultDecode.js

@@ -0,0 +1,19 @@
+"use strict";
+/**
+ * @file Thin salsa wrapper around cumin's PACS query result decoder.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pacsQuery_resultDecode = pacsQuery_resultDecode;
+const cumin_1 = require("@fnndsc/cumin");
+/**
+ * Decode the result payload of a PACS query by ID.
+ *
+ * @param queryId - PACS query ID.
+ * @returns Result containing decoded payload (raw, decoded buffers/text/json) or Err.
+ */
+async function pacsQuery_resultDecode(queryId) {
+    return (0, cumin_1.pacsQuery_resultDecode)(queryId);
+}
+//# sourceMappingURL=resultDecode.js.map

package/dist/pacs/resultDecode.js.map

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