@fnndsc/brasa 0.9.2 → 0.10.0

package/dist/builtins/net/status.js

@@ -0,0 +1,210 @@
+/**
+ * @file Builtin `pacs status`.
+ *
+ * Reports, per series, how much of a PACS query's data has actually landed in
+ * CUBE storage: a fill bar of registered files against the expected DICOM
+ * instance count, the derived state (pending/pulling/pulled), and the in-CUBE
+ * `/SERVICES` folder each pulled series occupies. This is the observability
+ * half of the pull recovery loop: `pacs status` shows what is missing, and
+ * re-running `pull` fetches exactly that.
+ *
+ * The target may be a query expression (`AccessionNumber:22119730`), a
+ * `/net/pacs/queries/...` VFS path, or a bare numeric query id. An expression
+ * is matched against the caller's existing PACS queries (most recent wins) so
+ * repeated status checks do not mint new query records; only when no match
+ * exists is a fresh query created.
+ *
+ * @module
+ */
+import chalk from 'chalk';
+import { pacsQueries_list, pacsRetrieve_statusForQuery, envelope_ok, envelope_error, } from '@fnndsc/cumin';
+import { args_checkHasHelpFlag, help_render } from '../help.js';
+import { spinner } from '../../lib/spinner.js';
+import { pacsQuery_createAndWait, queryExpr_parse } from './query.js';
+import { queryId_extractFromFolder } from '@fnndsc/salsa';
+import { pacsServer_resolve } from './pacsUtils.js';
+/** Width of the per-series fill bar, in characters. */
+const BAR_WIDTH = 20;
+/**
+ * Renders a fill bar for a series' progress.
+ *
+ * @param actual - Files registered in CUBE.
+ * @param expected - Files the PACS reports for the series.
+ * @returns A `▓▓▓░░░`-style bar of {@link BAR_WIDTH} characters.
+ */
+function bar_render(actual, expected) {
+    const denominator = Math.max(expected, actual, 1);
+    const filled = Math.min(BAR_WIDTH, Math.round((actual / denominator) * BAR_WIDTH));
+    return `${'▓'.repeat(filled)}${'░'.repeat(BAR_WIDTH - filled)}`;
+}
+/**
+ * Colors a series line by its retrieve state.
+ *
+ * @param status - The series' derived state.
+ * @param text - The rendered line.
+ * @returns The line, colored: pulled green, pulling yellow, pending gray,
+ *   error red.
+ */
+function seriesLine_colorize(status, text) {
+    if (status === 'pulled')
+        return chalk.green(text);
+    if (status === 'pulling')
+        return chalk.yellow(text);
+    if (status === 'error')
+        return chalk.red(text);
+    return chalk.gray(text);
+}
+/**
+ * Finds the caller's most recent PACS query whose stored expression matches
+ * the given one.
+ *
+ * Queries store their expression as canonical JSON of the parsed key/value
+ * map, so matching compares parsed objects rather than raw strings.
+ *
+ * @param exprObj - The parsed query expression.
+ * @returns The highest (most recent) matching query id, or null when none
+ *   matches.
+ */
+async function queryId_findForExpression(exprObj) {
+    const listResult = await pacsQueries_list({ limit: 200, offset: 0 });
+    if (!listResult.ok || !listResult.value)
+        return null;
+    const listing = listResult.value;
+    const rows = listing.tableData ?? [];
+    let bestId = null;
+    for (const row of rows) {
+        const rawQuery = row.query;
+        const id = Number(row.id);
+        if (typeof rawQuery !== 'string' || !Number.isInteger(id))
+            continue;
+        let stored;
+        try {
+            stored = JSON.parse(rawQuery);
+        }
+        catch {
+            continue;
+        }
+        const storedKeys = Object.keys(stored ?? {});
+        const exprKeys = Object.keys(exprObj);
+        const matches = storedKeys.length === exprKeys.length &&
+            exprKeys.every((key) => stored[key] === exprObj[key]);
+        if (matches && (bestId === null || id > bestId))
+            bestId = id;
+    }
+    return bestId;
+}
+/**
+ * Resolves a status target to a numeric query id.
+ *
+ * @param target - A bare query id, a `/net/pacs/queries/...` path, or a query
+ *   expression.
+ * @param pacsserver - The resolved PACS server identifier, used only when a
+ *   fresh query must be created for an unmatched expression.
+ * @returns The query id, or null when the target cannot be resolved (an error
+ *   line has been rendered by the caller from the returned reason).
+ */
+async function statusTarget_resolve(target, pacsserver) {
+    if (/^\d+$/.test(target)) {
+        return { queryId: Number(target), reason: '' };
+    }
+    if (target.startsWith('/')) {
+        const parsedId = queryId_extractFromFolder(target);
+        if (!Number.isNaN(parsedId))
+            return { queryId: parsedId, reason: '' };
+        return { queryId: null, reason: `Cannot parse a query id from path: ${target}` };
+    }
+    const exprObj = queryExpr_parse(target);
+    if (!exprObj) {
+        return { queryId: null, reason: `Not a query id, PACS path, or query expression: ${target}` };
+    }
+    const existing = await queryId_findForExpression(exprObj);
+    if (existing !== null)
+        return { queryId: existing, reason: '' };
+    // No prior query for this expression: run one so status has a series list
+    // to compare against.
+    spinner.start(`Querying PACS for ${target}...`, true);
+    const created = await pacsQuery_createAndWait(target, `status_${target}`, pacsserver, (msg) => spinner.updateMessage(msg));
+    spinner.stop();
+    if (!created)
+        return { queryId: null, reason: `Query failed for: ${target}` };
+    return { queryId: created.queryId, reason: '' };
+}
+/**
+ * Renders a status report: per study, one bar line per series with counts,
+ * state, and the in-CUBE folder path.
+ *
+ * @param report - The status report to render.
+ * @returns The rendered multi-line report.
+ */
+function statusReport_render(report) {
+    const lines = [];
+    let pulledCount = 0;
+    let seriesCount = 0;
+    for (const study of report.studies) {
+        lines.push(chalk.bold(`Study: ${study.studyDescription ?? study.studyInstanceUID ?? 'unknown'}`));
+        const descWidth = Math.max(...study.series.map((s) => (s.seriesDescription ?? s.seriesInstanceUID).length), 1);
+        for (const series of study.series) {
+            seriesCount++;
+            if (series.status === 'pulled')
+                pulledCount++;
+            const desc = (series.seriesDescription ?? series.seriesInstanceUID).padEnd(descWidth);
+            const bar = bar_render(series.actualFiles, series.expectedFiles);
+            const counts = `${series.actualFiles}/${series.expectedFiles}`.padStart(9);
+            const state = series.status.padEnd(7);
+            lines.push(seriesLine_colorize(series.status, `  ${desc}  ${bar} ${counts}  ${state}`));
+            if (series.folderPath !== null) {
+                lines.push(chalk.gray(`  ${' '.repeat(descWidth)}  ${series.folderPath}`));
+            }
+        }
+        lines.push('');
+    }
+    const summaryColor = pulledCount === seriesCount ? chalk.green : chalk.yellow;
+    lines.push(summaryColor(`${pulledCount}/${seriesCount} series fully in CUBE.`));
+    if (pulledCount < seriesCount) {
+        lines.push(chalk.gray(`Re-run pull to fetch the missing series; already-complete series are skipped.`));
+    }
+    return `${lines.join('\n')}\n`;
+}
+/**
+ * Reports per-series pull status for a PACS query: expected vs registered
+ * file counts, derived state, and the in-CUBE storage path.
+ *
+ * @param args - `[target]` where target is a query expression, a
+ *   `/net/pacs/queries/...` path, or a numeric query id.
+ * @returns An envelope carrying the rendered report and a typed model of it.
+ * @example
+ * pacs status AccessionNumber:22119730
+ * pacs status /net/pacs/queries/AccessionNumber:22119730_qid:2833
+ * pacs status 2833
+ */
+export async function builtin_pacsStatus(args) {
+    if (args_checkHasHelpFlag(args, 'pacs')) {
+        return envelope_ok(help_render('pacs'));
+    }
+    const target = args.find((a) => !a.startsWith('--'));
+    if (!target) {
+        process.exitCode = 1;
+        return envelope_error('', undefined, `${chalk.red('pacs status: Missing target. Usage: pacs status <expression | path | queryId>')}\n`);
+    }
+    const pacsserver = await pacsServer_resolve(null);
+    if (!pacsserver) {
+        process.exitCode = 1;
+        return envelope_error('', undefined, `${chalk.red('pacs status: No PACS server available. Set one with: pacs connect <id>')}\n`);
+    }
+    const { queryId, reason } = await statusTarget_resolve(target, pacsserver);
+    if (queryId === null) {
+        process.exitCode = 1;
+        return envelope_error('', undefined, `${chalk.red(`pacs status: ${reason}`)}\n`);
+    }
+    spinner.start(`Resolving CUBE storage for query ${queryId}...`, true);
+    const reportResult = await pacsRetrieve_statusForQuery(queryId);
+    spinner.stop();
+    if (!reportResult.ok) {
+        process.exitCode = 1;
+        return envelope_error('', undefined, `${chalk.red(`pacs status: Failed to build status report for query ${queryId}.`)}\n`);
+    }
+    const report = reportResult.value;
+    const rendered = `${chalk.bold(`Query ${queryId}`)}\n${statusReport_render(report)}`;
+    return envelope_ok(rendered, { kind: 'pacs.status', data: report });
+}
+//# sourceMappingURL=status.js.map

package/dist/builtins/net/status.js.map

@@ -0,0 +1 @@
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package/dist/builtins/pluginExecute.d.ts

@@ -6,6 +6,7 @@
  *
  * @module
  */
+import { type CommandEnvelope } from '@fnndsc/cumin';
 /**
  * Executes a plugin in the current directory context.
  *
@@ -14,7 +15,7 @@
  *
  * @param pluginName - Full plugin name with version (e.g., pl-dcm2niix-v2.1.1).
  * @param args - Array of command line arguments.
- * @returns Promise that resolves when execution completes.
+ * @returns Command envelope whose status matches parsing and execution.
  *
  * @example
  * ```typescript
@@ -24,4 +25,4 @@
  * ]);
  * ```
  */
-export declare function builtin_executePlugin(pluginName: string, args: string[]): Promise<void>;
+export declare function builtin_executePlugin(pluginName: string, args: string[]): Promise<CommandEnvelope>;

package/dist/builtins/pluginExecute.js

@@ -7,33 +7,14 @@
  * @module
  */
 import { plugin_executeInPlace } from '@fnndsc/salsa';
-import { dictionary_fromCLI, errorStack, procCache_get } from '@fnndsc/cumin';
+import { errorStack, procCache_get, envelope_error, envelope_ok, } from '@fnndsc/cumin';
 import chalk from 'chalk';
 import { session } from '../session/index.js';
 import { vfs } from '../lib/vfs/vfs.js';
-/**
- * Parses a plugin name from /bin format (name-vVersion) into ChRIS search format.
- *
- * @param pluginName - Plugin name in format: pl-name-vX.Y.Z
- * @returns Search string in format: name_exact:pl-name,version:X.Y.Z
- *
- * @example
- * ```typescript
- * pluginName_toSearchString('pl-dcm2niix-v1.0.2')
- * // Returns: 'name_exact:pl-dcm2niix,version:1.0.2'
- * ```
- */
-function pluginName_toSearchString(pluginName) {
-    // Pattern: (name)-v(version)
-    const match = pluginName.match(/^(.+)-v(.+)$/);
-    if (match) {
-        const name = match[1];
-        const version = match[2];
-        return `name_exact:${name},version:${version}`;
-    }
-    // Fallback: if no version suffix, search by name only
-    return `name_exact:${pluginName}`;
-}
+import { newFeed_cacheAdd } from './feedCreation.js';
+import { executableArguments_parse } from './argumentTokens.js';
+import { pluginSelector_normalize } from './pluginSelector.js';
+import { sink_dataLine, sink_errLine } from '../core/sink.js';
 /**
  * Executes a plugin in the current directory context.
  *
@@ -42,7 +23,7 @@ function pluginName_toSearchString(pluginName) {
  *
  * @param pluginName - Full plugin name with version (e.g., pl-dcm2niix-v2.1.1).
  * @param args - Array of command line arguments.
- * @returns Promise that resolves when execution completes.
+ * @returns Command envelope whose status matches parsing and execution.
  *
  * @example
  * ```typescript
@@ -54,88 +35,76 @@ function pluginName_toSearchString(pluginName) {
  */
 export async function builtin_executePlugin(pluginName, args) {
     try {
-        // 1. Parse arguments - split on '--' delimiter
-        const argsString = args.join(' ');
-        let pluginArgsStr = argsString;
-        let contextArgsStr = '';
-        // Check for ' -- ' delimiter (space-dash-dash-space)
-        const delimiterIndex = argsString.indexOf(' -- ');
-        if (delimiterIndex !== -1) {
-            pluginArgsStr = argsString.substring(0, delimiterIndex);
-            contextArgsStr = argsString.substring(delimiterIndex + 4); // +4 to skip ' -- '
-        }
+        // 1. Split the already-tokenized arguments on the context delimiter.
+        const delimiterIndex = args.indexOf('--');
+        const pluginArgTokens = delimiterIndex === -1 ? args : args.slice(0, delimiterIndex);
+        const contextArgTokens = delimiterIndex === -1 ? [] : args.slice(delimiterIndex + 1);
         // 2. Parse both sets of parameters
         let pluginParams = {};
         let contextParams = {};
-        if (pluginArgsStr.trim()) {
+        if (pluginArgTokens.length > 0) {
             try {
-                pluginParams = dictionary_fromCLI(pluginArgsStr);
+                pluginParams = executableArguments_parse(pluginArgTokens);
             }
             catch (e) {
                 const msg = e instanceof Error ? e.message : String(e);
-                console.error(chalk.red(`Error parsing plugin parameters: ${msg}`));
-                return;
+                sink_errLine(chalk.red(`Error parsing plugin parameters: ${msg}`));
+                return envelope_error('');
             }
         }
-        if (contextArgsStr.trim()) {
+        if (contextArgTokens.length > 0) {
             try {
-                contextParams = dictionary_fromCLI(contextArgsStr);
+                contextParams = executableArguments_parse(contextArgTokens);
             }
             catch (e) {
                 const msg = e instanceof Error ? e.message : String(e);
-                console.error(chalk.red(`Error parsing context parameters: ${msg}`));
-                return;
+                sink_errLine(chalk.red(`Error parsing context parameters: ${msg}`));
+                return envelope_error('');
             }
         }
         // 3. Set default context params if not provided
         const cwd = await session.getCWD();
         const isInFeed = cwd.includes('/feeds/feed_');
         // If no context params provided and not in a feed, use directory name as feed title
-        if (!contextArgsStr && !isInFeed) {
+        if (contextArgTokens.length === 0 && !isInFeed) {
             const defaultTitle = cwd.split('/').pop() || 'Untitled';
             contextParams.feed_title = defaultTitle;
-            console.log(chalk.cyan(`Using feed title: "${defaultTitle}" (customize with -- feed_title="Custom Title")`));
+            sink_dataLine(chalk.cyan(`Using feed title: "${defaultTitle}" (customize with -- feed_title="Custom Title")`));
         }
         // 4. Get /bin listing for finding pl-dircopy
         const binResult = await vfs.data_get('/bin');
         if (!binResult.ok) {
-            console.error(chalk.red('Failed to access /bin directory'));
-            return;
+            sink_errLine(chalk.red('Failed to access /bin directory'));
+            return envelope_error('');
         }
         const binListing = binResult.value.map((item) => item.name);
         // 5. Convert plugin name from /bin format to ChRIS search format
         // Example: pl-dcm2niix-v1.0.2 → name_exact:pl-dcm2niix,version:1.0.2
-        const pluginSearchString = pluginName_toSearchString(pluginName);
+        const pluginSearchString = pluginSelector_normalize(pluginName);
         // 6. Execute via salsa
         const result = await plugin_executeInPlace(pluginSearchString, pluginParams, contextParams, cwd, binListing);
         if (!result) {
             // Display all errors from the stack for better debugging
-            console.error(chalk.red('Plugin execution failed:'));
+            sink_errLine(chalk.red('Plugin execution failed:'));
             let error = errorStack.stack_pop();
             while (error) {
-                console.error(chalk.red(`  - ${error.message}`));
+                sink_errLine(chalk.red(`  - ${error.message}`));
                 error = errorStack.stack_pop();
             }
-            return;
+            return envelope_error('');
         }
         // 7. Push to procCache so /proc reflects new jobs immediately
         if (result.feedID !== undefined && result.dircopyInstanceID !== undefined) {
             // New feed: push dircopy root node + plugin node
-            const feedTitle = cwd.split('/').pop() || `feed_${result.feedID}`;
-            procCache_get().feed_add({
-                id: result.feedID, title: feedTitle,
-                ownerUsername: cwd.split('/')[2] ?? '', public: false,
-                creationDate: new Date().toISOString(),
-                finishedJobs: 0, erroredJobs: 0, startedJobs: 0,
-                scheduledJobs: 2, cancelledJobs: 0, createdJobs: 0,
-            });
-            procCache_get().instance_add({
-                id: result.dircopyInstanceID, feedID: result.feedID,
-                parentID: null, pluginName: 'pl-dircopy', params: null, status: 'scheduled',
-            });
-            procCache_get().instance_add({
-                id: result.pluginInstanceID, feedID: result.feedID,
-                parentID: result.dircopyInstanceID, pluginName: result.pluginName, params: null, status: 'scheduled',
+            const feedTitle = typeof contextParams.feed_title === 'string'
+                ? contextParams.feed_title
+                : cwd.split('/').pop() || `feed_${result.feedID}`;
+            newFeed_cacheAdd({
+                feedID: result.feedID,
+                title: feedTitle,
+                ownerUsername: cwd.split('/')[2] ?? '',
+                rootInstanceID: result.dircopyInstanceID,
+                child: { id: result.pluginInstanceID, pluginName: result.pluginName },
             });
         }
         else if (result.parentID !== null) {
@@ -153,14 +122,16 @@ export async function builtin_executePlugin(pluginName, args) {
         }
         // 8. Render output
         if (result.feedID) {
-            console.log(chalk.green(`Feed created: ${result.feedID}`));
+            sink_dataLine(chalk.green(`Feed created: ${result.feedID}`));
         }
-        console.log(chalk.green(`Job scheduled: ${pluginName} (ID: ${result.pluginInstanceID})`));
-        console.log(chalk.cyan(`Output will be in: ${result.outputPath}`));
+        sink_dataLine(chalk.green(`Job scheduled: ${pluginName} (ID: ${result.pluginInstanceID})`));
+        sink_dataLine(chalk.cyan(`Output will be in: ${result.outputPath}`));
+        return envelope_ok('');
     }
     catch (error) {
         const msg = error instanceof Error ? error.message : String(error);
-        console.error(chalk.red(`Error executing plugin: ${msg}`));
+        sink_errLine(chalk.red(`Error executing plugin: ${msg}`));
+        return envelope_error('');
     }
 }
 //# sourceMappingURL=pluginExecute.js.map

package/dist/builtins/pluginExecute.js.map

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package/dist/builtins/pluginSelector.d.ts

@@ -0,0 +1,15 @@
+/**
+ * @file Shared normalization for plugin executable selectors.
+ *
+ * Direct execution and composite commands use this module to resolve `/bin`-style
+ * plugin names through the same exact-name and optional-version query grammar.
+ *
+ * @module
+ */
+/**
+ * Normalize a `/bin` plugin name into a ChRIS plugin search selector.
+ *
+ * @param selector - Plugin name, optionally ending in `-v<version>`.
+ * @returns Exact-name selector with an exact version when one was supplied.
+ */
+export declare function pluginSelector_normalize(selector: string): string;

package/dist/builtins/pluginSelector.js

@@ -0,0 +1,21 @@
+/**
+ * @file Shared normalization for plugin executable selectors.
+ *
+ * Direct execution and composite commands use this module to resolve `/bin`-style
+ * plugin names through the same exact-name and optional-version query grammar.
+ *
+ * @module
+ */
+/**
+ * Normalize a `/bin` plugin name into a ChRIS plugin search selector.
+ *
+ * @param selector - Plugin name, optionally ending in `-v<version>`.
+ * @returns Exact-name selector with an exact version when one was supplied.
+ */
+export function pluginSelector_normalize(selector) {
+    const match = selector.match(/^(.+)-v(.+)$/);
+    if (match === null)
+        return `name_exact:${selector}`;
+    return `name_exact:${match[1]},version:${match[2]}`;
+}
+//# sourceMappingURL=pluginSelector.js.map

package/dist/builtins/pluginSelector.js.map

@@ -0,0 +1 @@
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