@fnndsc/brasa 0.11.1 → 0.13.0

package/dist/buildinfo.json

@@ -1 +1 @@
-{"hash":"752c98"}
+{"hash":"03f466"}

package/dist/builtins/fs/archive.d.ts

@@ -0,0 +1,43 @@
+/**
+ * @file Archiving a directory so it can leave CUBE as one file.
+ *
+ * CUBE serves a file's bytes but has no representation of a directory, so a
+ * client that wants a copy of a tree must build one. The platform's own answer
+ * is a registered pipeline — `pl-dircopy` into a zip plugin — and using it is
+ * right: making an archive is a computation, and computations here are
+ * plugins. What is wrong is where that orchestration has historically lived.
+ * The ChRIS web UI carried it in a saga, so no other client could reuse it,
+ * and a presentation layer became an orchestrator. Here it is an intent, in
+ * the kernel, reached identically by every surface.
+ *
+ * The cost is real and worth stating: an archive run creates a feed, so the
+ * compute graph records a copy as though it were an analysis step. That is a
+ * CUBE gap, filed as issue #233, not a design choice — the day CUBE can hand
+ * over a directory, this module is deleted.
+ *
+ * @module
+ */
+/**
+ * The archive a run produced.
+ *
+ * @property path - The archive's path in the session's namespace.
+ * @property filename - Its basename, for a surface to suggest at the destination.
+ * @property size - Its size in bytes, when the listing reported one.
+ */
+export interface ArchiveResult {
+    path: string;
+    filename: string;
+    size?: number;
+}
+/**
+ * Archives a directory into a single file inside CUBE.
+ *
+ * Announces what it is doing, because it is a workaround and a silent one
+ * would leave the operator wondering why a feed appeared: see
+ * link:../../../../docs/CUBE-gaps.adoc[CUBE-gaps.adoc].
+ *
+ * @param directory - The directory to archive, already resolved.
+ * @returns The archive, or null when the run could not complete. Reasons are
+ *   pushed to the error stack.
+ */
+export declare function directory_archive(directory: string): Promise<ArchiveResult | null>;

package/dist/builtins/fs/archive.js

@@ -0,0 +1,174 @@
+/**
+ * @file Archiving a directory so it can leave CUBE as one file.
+ *
+ * CUBE serves a file's bytes but has no representation of a directory, so a
+ * client that wants a copy of a tree must build one. The platform's own answer
+ * is a registered pipeline — `pl-dircopy` into a zip plugin — and using it is
+ * right: making an archive is a computation, and computations here are
+ * plugins. What is wrong is where that orchestration has historically lived.
+ * The ChRIS web UI carried it in a saga, so no other client could reuse it,
+ * and a presentation layer became an orchestrator. Here it is an intent, in
+ * the kernel, reached identically by every surface.
+ *
+ * The cost is real and worth stating: an archive run creates a feed, so the
+ * compute graph records a copy as though it were an analysis step. That is a
+ * CUBE gap, filed as issue #233, not a design choice — the day CUBE can hand
+ * over a directory, this module is deleted.
+ *
+ * @module
+ */
+import chalk from 'chalk';
+import { errorStack } from '@fnndsc/cumin';
+import { feed_create, files_listRecursive, job_statusFetch, feed_delete, pipeline_readiness, pipeline_run, } from '@fnndsc/salsa';
+import { sink_get } from '../../core/sink.js';
+import { vfs } from '../../lib/vfs/vfs.js';
+/**
+ * The registered pipeline that produces the archive.
+ *
+ * Named rather than assembled: a pipeline is the platform's unit of composed
+ * work and is what a deployment actually registers. `CHRIS_ARCHIVE_PIPELINE`
+ * overrides it, because the name carries a version stamp and a given CUBE may
+ * have registered a different one.
+ */
+const ARCHIVE_PIPELINE = process.env['CHRIS_ARCHIVE_PIPELINE'] ?? 'zip v20240311';
+/** How often the archive job's status is checked, in milliseconds. */
+const POLL_INTERVAL_MS = 2000;
+/** How long to wait before giving up on the archive job, in milliseconds. */
+const POLL_TIMEOUT_MS = 15 * 60 * 1000;
+/** Terminal job states, successful or not. */
+const SETTLED = [
+    'finishedSuccessfully', 'finishedWithError', 'cancelled',
+];
+/**
+ * Waits for a plugin instance to reach a terminal state.
+ *
+ * @param instanceId - The instance to watch.
+ * @param label - What to call it while reporting progress.
+ * @returns The terminal status, or null when it never settled.
+ */
+async function instance_settle(instanceId, label) {
+    const deadline = Date.now() + POLL_TIMEOUT_MS;
+    while (Date.now() < deadline) {
+        const status = await job_statusFetch(instanceId);
+        if (status.ok && SETTLED.includes(status.value)) {
+            return status.value;
+        }
+        sink_get().progress_write({
+            operation: 'task',
+            kind: 'inspection',
+            phase: 'working',
+            label: `${label} — ${status.ok ? status.value : 'waiting'}`,
+        });
+        await new Promise((resolve) => { setTimeout(resolve, POLL_INTERVAL_MS); });
+    }
+    return null;
+}
+/**
+ * Archives a directory into a single file inside CUBE.
+ *
+ * Announces what it is doing, because it is a workaround and a silent one
+ * would leave the operator wondering why a feed appeared: see
+ * link:../../../../docs/CUBE-gaps.adoc[CUBE-gaps.adoc].
+ *
+ * @param directory - The directory to archive, already resolved.
+ * @returns The archive, or null when the run could not complete. Reasons are
+ *   pushed to the error stack.
+ */
+export async function directory_archive(directory) {
+    const name = directory.split('/').filter(Boolean).pop() ?? 'archive';
+    const bin = await vfs.data_get('/bin');
+    if (!bin.ok || !bin.value.some((item) => item.name.startsWith('pl-dircopy'))) {
+        errorStack.stack_push('error', 'pl-dircopy is not registered on this CUBE, so no feed can be created and no directory archived.');
+        return null;
+    }
+    // Ask whether the pipeline can run before creating anything. Preparing it
+    // needs no feed, and a feed created for a run that never happens is litter
+    // on someone's CUBE that nobody knows to clean up.
+    const readiness = await pipeline_readiness(ARCHIVE_PIPELINE);
+    if (!readiness.ready) {
+        errorStack.stack_push('error', readiness.reason === 'unregistered'
+            ? `The '${ARCHIVE_PIPELINE}' pipeline is not registered on this CUBE, so a directory cannot be archived. ` +
+                'Register it from the ChRIS store, or set CHRIS_ARCHIVE_PIPELINE to one that is.'
+            : `The '${ARCHIVE_PIPELINE}' pipeline is registered but cannot run here — see the reason above, which is ` +
+                'usually a node not registered on the target compute environment. Fix that, or set ' +
+                'CHRIS_ARCHIVE_PIPELINE to a pipeline that can run.');
+        return null;
+    }
+    sink_get().status_write(`${chalk.yellow('⚠ CUBE cannot hand over a directory, so this runs the ')}` +
+        `${chalk.bold(ARCHIVE_PIPELINE)}${chalk.yellow(' pipeline to make an archive first.')}\n` +
+        `${chalk.gray('  That creates a feed. See docs/CUBE-gaps.adoc and issue 233.')}\n`);
+    const feed = await feed_create([directory], { title: `Archive of ${name}` });
+    if (!feed) {
+        errorStack.stack_push('error', `Could not create a feed to archive ${directory}.`);
+        return null;
+    }
+    const dircopyId = feed.pluginInstance.data.id;
+    const workflow = await pipeline_run(ARCHIVE_PIPELINE, dircopyId);
+    if (!workflow.ok || workflow.value.pluginInstanceIds.length === 0) {
+        // Readiness passed, so this failed between then and now. Say what was left
+        // behind rather than overwriting a reason the stack already carries.
+        await feed_discard(feed.id, name);
+        return null;
+    }
+    const archiveInstanceId = workflow.value.pluginInstanceIds[0];
+    const status = await instance_settle(archiveInstanceId, `Archiving ${name}`);
+    sink_get().progress_write({ operation: 'task', kind: 'inspection', phase: 'complete' });
+    if (status === null) {
+        errorStack.stack_push('error', `Archiving ${name} did not finish within the time allowed.`);
+        // The run may yet finish, so its feed is left alone rather than deleted
+        // out from under a job that is still going.
+        return null;
+    }
+    if (status !== 'finishedSuccessfully') {
+        errorStack.stack_push('error', `Archiving ${name} ended as ${status}.`);
+        await feed_discard(feed.id, name);
+        return null;
+    }
+    return archiveOutput_find(feed.id, dircopyId, archiveInstanceId, name);
+}
+/**
+ * Removes a feed created for an archive run that then failed.
+ *
+ * The feed exists only to root the archive. Left behind it is litter in
+ * someone's feed list and a copy in the compute graph asserting an analysis
+ * that produced nothing — so it is removed, and named when it cannot be.
+ *
+ * @param feedId - The feed to discard.
+ * @param name - The directory's name, for the message.
+ */
+async function feed_discard(feedId, name) {
+    const removed = await feed_delete(feedId);
+    errorStack.stack_push('error', removed
+        ? `Archiving ${name} failed; the feed it created was removed.`
+        : `Archiving ${name} failed, and feed ${feedId} could not be removed. Delete it when convenient.`);
+}
+/**
+ * Locates the file an archive run produced.
+ *
+ * The output directory is listed rather than its path reconstructed: the
+ * archive's name is the pipeline's business, and a client that guesses it
+ * breaks the day the pipeline changes.
+ *
+ * @param feedId - The feed the run created.
+ * @param dircopyId - The `pl-dircopy` instance that rooted it.
+ * @param archiveInstanceId - The instance that produced the archive.
+ * @param name - The directory's name, for the error message.
+ * @returns The archive, or null when the output directory held no file.
+ */
+async function archiveOutput_find(feedId, dircopyId, archiveInstanceId, name) {
+    const outputRoot = `feeds/feed_${feedId}/pl-dircopy_${dircopyId}`;
+    const items = await files_listRecursive(outputRoot);
+    const produced = items.filter((item) => item.path.includes(`_${archiveInstanceId}/data/`) && item.type !== 'dir');
+    if (produced.length === 0) {
+        errorStack.stack_push('error', `The archive of ${name} produced no file.`);
+        return null;
+    }
+    const archive = produced[0];
+    const filename = archive.path.split('/').filter(Boolean).pop() ?? `${name}.zip`;
+    return {
+        path: archive.path,
+        filename,
+        ...(typeof archive.size === 'number' ? { size: archive.size } : {}),
+    };
+}
+//# sourceMappingURL=archive.js.map

package/dist/builtins/fs/archive.js.map

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

@@ -1,6 +1,7 @@
 import { type CommandEnvelope } from '@fnndsc/cumin';
 /**
- * Downloads a remote ChRIS file or directory to the local filesystem.
+ * Downloads a remote ChRIS file or directory to the local filesystem, or hands
+ * it to the surface when the engine's disk is not the operator's.
  *
  * @param args - [remotePathOrGlob, localPath] plus optional -f/--force to overwrite.
  * @returns An envelope carrying the download summary.

package/dist/builtins/fs/download.js

@@ -5,11 +5,13 @@
 import path from 'path';
 import chalk from 'chalk';
 import { files_downloadWithProgress as chefs_download_cmd, files_downloadManyWithProgress as chefs_downloadMany_cmd, bytes_format } from '@fnndsc/chili/commands/fs/download.js';
-import { envelope_ok, envelope_error } from '@fnndsc/cumin';
+import { envelope_ok, envelope_error, errorStack } from '@fnndsc/cumin';
 import { sink_get } from '../../core/sink.js';
 import { shellArguments_pathnameExpanded } from '../../lib/parser.js';
 import { path_resolve } from '../utils.js';
 import { surface_get } from '../../core/surface.js';
+import { files_path_isDirectory, files_listRecursive } from '@fnndsc/salsa';
+import { directory_archive } from './archive.js';
 /**
  * Asks the issuing surface to confirm a local download overwrite or merge.
  *
@@ -24,7 +26,100 @@ async function downloadConfirmation_request(message) {
     }
 }
 /**
- * Downloads a remote ChRIS file or directory to the local filesystem.
+ * Hands each requested file to the surface, for a session whose engine runs
+ * somewhere its operator is not.
+ *
+ * Only the request travels: the surface fetches the bytes itself, through
+ * whichever route suits it. Multiple sources become multiple deliveries, since
+ * a surface with no filesystem — a browser — has no directory to fill.
+ *
+ * @param surface - The surface running this command.
+ * @param sourceArgs - The requested source paths, before resolution.
+ * @param destination - Where the operator asked for it. A surface with a
+ *   filesystem treats an existing directory as a place to fill and anything
+ *   else as the filename; a surface without one ignores it.
+ * @returns An envelope summarising where the files landed.
+ */
+async function surfaceDownload_run(surface, sourceArgs, destination) {
+    if (!surface.capabilities.fileDelivery) {
+        process.exitCode = 1;
+        return envelope_error('', undefined, `${chalk.red('download: this surface cannot receive a file, and the engine will not write to its own host.')}\n`);
+    }
+    const sources = await Promise.all(sourceArgs.map(path_resolve));
+    // A directory has no bytes to hand over, and what to do about that depends on
+    // what the surface has. A shell — remote or not — owns a filesystem, so it
+    // receives the tree file by file and gets the folder it asked for. A browser
+    // owns no directory and can only take files one at a time, so several hundred
+    // DICOM instances would be several hundred saves; for that surface alone the
+    // directory is archived into one CUBE file first. See issue #233 for why an
+    // archive is a workaround rather than a feature.
+    const targets = [];
+    for (const source of sources) {
+        if (!(await files_path_isDirectory(source))) {
+            targets.push({ path: source, filename: source.split('/').filter(Boolean).pop() ?? 'download' });
+            continue;
+        }
+        if (surface.capabilities.localFilesystem) {
+            const items = await files_listRecursive(source);
+            for (const item of items) {
+                if (item.type === 'dir')
+                    continue;
+                targets.push({
+                    path: item.path,
+                    // Keep the tree: a surface with directories reproduces the shape
+                    // under the destination rather than flattening it.
+                    filename: item.path.startsWith(source)
+                        ? item.path.slice(source.length).replace(/^\/+/, '')
+                        : (item.path.split('/').filter(Boolean).pop() ?? 'download'),
+                    ...(typeof item.size === 'number' ? { size: item.size } : {}),
+                });
+            }
+            continue;
+        }
+        const archived = await directory_archive(source);
+        if (!archived) {
+            process.exitCode = 1;
+            const reasons = errorStack.stack_getAll?.()
+                .map((entry) => typeof entry === 'string' ? entry : (entry.message ?? String(entry)))
+                .join('\n  ') ?? '';
+            return envelope_error('', undefined, `${chalk.red(`download: could not archive ${source}.`)}\n${reasons ? `  ${chalk.red(reasons)}\n` : ''}`);
+        }
+        targets.push(archived);
+    }
+    const delivered = [];
+    const failed = [];
+    for (const target of targets) {
+        const filename = target.filename;
+        try {
+            const result = await surface.fileDeliver({
+                path: target.path,
+                filename,
+                destination,
+                ...(target.size !== undefined ? { size: target.size } : {}),
+            });
+            delivered.push(`${chalk.gray(`  ${filename} → ${result.location}`)} ${chalk.gray(`(${bytes_format(result.bytes)})`)}`);
+        }
+        catch (error) {
+            const reason = error instanceof Error ? error.message : String(error);
+            failed.push(`${chalk.red(`  ${filename}: ${reason}`)}`);
+        }
+    }
+    let rendered = '\n';
+    if (failed.length === 0) {
+        rendered += `${chalk.green(`✓ Delivered ${delivered.length} file(s)`)}\n`;
+    }
+    else {
+        rendered += `${chalk.yellow(`⚠ Delivered ${delivered.length} file(s), ${failed.length} failed`)}\n`;
+        process.exitCode = 1;
+    }
+    rendered += [...delivered, ...failed].join('\n');
+    if (delivered.length > 0 || failed.length > 0)
+        rendered += '\n';
+    return failed.length === 0 ? envelope_ok(rendered) : envelope_error(rendered, undefined, '');
+}
+/**
+ * Downloads a remote ChRIS file or directory to the local filesystem, or hands
+ * it to the surface when the engine's disk is not the operator's.
  *
  * @param args - [remotePathOrGlob, localPath] plus optional -f/--force to overwrite.
  * @returns An envelope carrying the download summary.
@@ -45,6 +140,17 @@ export async function builtin_download(args) {
     const sourceWasExpanded = positionalIndexes
         .slice(0, -1)
         .some((index) => shellArguments_pathnameExpanded(args, index));
+    // A path resolved here is a path on the *engine's* disk. That is the
+    // operator's disk only when a local shell hosts the engine in its own
+    // process; under a daemon it is a machine nobody attending the session is
+    // sitting at. So when the surface does not share the engine's filesystem,
+    // the file is handed to the surface, which puts it somewhere its operator
+    // can actually reach — the client's disk for a remote shell, the download
+    // manager for a browser.
+    const surface = surface_get();
+    if (!surface.capabilities.engineFilesystem) {
+        return surfaceDownload_run(surface, sourceArgs, localPathArg);
+    }
     const targetLocal = path.resolve(localPathArg);
     try {
         const progress = {

package/dist/builtins/fs/download.js.map

@@ -1 +1 @@
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package/dist/builtins/fs/pull.js

@@ -52,20 +52,38 @@ function pullEvents_make() {
     return {
         task: (task, status, phase) => pullProgress_emit(task, status, phase),
         retryRound: (attempt, retryMax, count) => sink_dataLine(chalk.yellow(`\nRetry ${attempt}/${retryMax} for ${count} unconfirmed series...`)),
+        // Said out loud: a silent reconnection during a long pull is
+        // indistinguishable from a stall, and this one takes seconds.
+        reconnect: (attempt, maxAttempts, watching) => sink_dataLine(chalk.gray(`  Retrieve watch reconnecting (${attempt}/${maxAttempts}) — ${watching} series still in flight; ` +
+            'the retrieves themselves are unaffected.')),
     };
 }
-function pullProgress_complete(allTasks, failed) {
+/**
+ * Closes the pull's progress channel with an honest terminal state.
+ *
+ * A pull that lost its watch is neither a success nor a failure: the surface
+ * should stop showing work in flight without claiming an outcome nobody
+ * observed.
+ *
+ * @param allTasks - Every task this pull covered.
+ * @param failed - Whether any series genuinely failed or was never fired.
+ * @param unconfirmed - How many series the watch stopped following.
+ */
+function pullProgress_complete(allTasks, failed, unconfirmed) {
     const done = allTasks.filter((t) => t.status === 'pulled').length;
+    const label = failed
+        ? 'Pull incomplete'
+        : (unconfirmed > 0 ? `Pull ended — ${unconfirmed} series unconfirmed` : 'Pull complete');
     sink_get().progress_write({
         operation: 'pull',
         kind: 'retrieve',
         phase: failed ? 'failed' : 'complete',
-        label: failed ? 'Pull incomplete' : 'Pull complete',
+        label,
         current: done,
         total: allTasks.length,
         percent: allTasks.length > 0 ? (done / allTasks.length) * 100 : 100,
         unit: 'series',
-        status: failed ? 'error' : 'done',
+        status: failed ? 'error' : (unconfirmed > 0 ? 'unconfirmed' : 'done'),
     });
 }
 /**
@@ -132,15 +150,19 @@ async function paths_resolveToVfs(paths, pacsserver) {
 function pullSummary_print(allTasks, totalFiringErrors) {
     const pulled = allTasks.filter((t) => t.status === 'pulled').length;
     const totalCount = allTasks.length;
-    const failures = allTasks.filter((t) => t.status !== 'pulled');
-    if (failures.length === 0) {
+    // Not seeing the end of a retrieve is not the same as it failing. The PACS
+    // keeps pushing and CUBE keeps registering after a watch drops, so a series
+    // the client lost sight of is reported as unknown rather than lost — and it
+    // does not fail the command, because nothing here knows that it failed.
+    const unconfirmed = allTasks.filter((t) => t.status === 'unconfirmed');
+    const failures = allTasks.filter((t) => t.status !== 'pulled' && t.status !== 'unconfirmed');
+    if (failures.length === 0 && unconfirmed.length === 0) {
         sink_dataLine(chalk.green(`\n✓ ${pulled}/${totalCount} series pulled successfully.`));
     }
     else {
-        sink_dataLine(chalk.yellow(`\n⚠ ${pulled}/${totalCount} series complete.`));
-        // An unfired series is permanent loss for this run (no retrieve exists,
-        // nothing will ever arrive); a watch failure is usually cosmetic — the
-        // PACS keeps pushing and CUBE keeps registering after detach.
+        sink_dataLine(chalk.yellow(`\n⚠ ${pulled}/${totalCount} series confirmed.`));
+        // An unfired series is permanent loss for this run: no retrieve exists, so
+        // nothing will ever arrive for it.
         for (const f of failures) {
             if (f.status === 'unfired') {
                 sink_dataLine(chalk.red(`  ✗ ${f.label} [FAILED TO FIRE — will not arrive; re-run pull]`));
@@ -149,13 +171,23 @@ function pullSummary_print(allTasks, totalFiringErrors) {
                 sink_dataLine(chalk.yellow(`  ✗ ${f.label} [${f.status.toUpperCase()} — verify with: pacs status]`));
             }
         }
-        process.exitCode = 1;
+        for (const u of unconfirmed) {
+            sink_dataLine(chalk.gray(`  ? ${u.label} [WATCH ENDED — may still be arriving; check with: pacs status]`));
+        }
+        if (unconfirmed.length > 0) {
+            sink_dataLine(chalk.gray(`  The retrieve watch ended before ${unconfirmed.length} series finished. ` +
+                'That is a lost connection, not a failed retrieve.'));
+        }
+        // Only a real failure fails the command.
+        if (failures.length > 0) {
+            process.exitCode = 1;
+        }
     }
     if (totalFiringErrors > 0) {
         sink_dataLine(chalk.red(`  ${totalFiringErrors} retrieve(s) were never fired — re-run pull to fetch them.`));
         process.exitCode = 1;
     }
-    pullProgress_complete(allTasks, failures.length > 0 || totalFiringErrors > 0);
+    pullProgress_complete(allTasks, failures.length > 0 || totalFiringErrors > 0, unconfirmed.length);
 }
 /**
  * Resolves the exact CUBE directories materialised by a completed pull.

package/dist/builtins/fs/pull.js.map

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package/dist/builtins/help.js

@@ -658,6 +658,11 @@ export const helpText = {
         description: 'Print the currently authenticated ChRIS username',
         examples: ['whoami'],
     },
+    version: {
+        usage: 'version',
+        description: 'Report the versions of the mise stack layers running this session',
+        examples: ['version'],
+    },
     id: {
         usage: 'id',
         description: 'Print the current CUBE user as a Unix-style UID, projected primary GID, and complete list of CUBE group memberships.',