@fnndsc/brasa 0.56.3 → 0.57.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fnndsc/brasa",
-  "version": "0.56.3",
+  "version": "0.57.0",
   "description": "BRASA Runs Abstracted Shell Actions - the hostable ChRIS shell engine (kernel)",
   "repository": {
     "type": "git",
@@ -48,10 +48,10 @@
   "author": "FNNDSC <dev@babyMRI.org>",
   "license": "MIT",
   "dependencies": {
-    "@fnndsc/chili": "^3.9.4",
-    "@fnndsc/fond": "^0.6.1",
-    "@fnndsc/cumin": "^3.30.5",
-    "@fnndsc/salsa": "^4.5.4",
+    "@fnndsc/chili": "^3.9.5",
+    "@fnndsc/fond": "^0.6.2",
+    "@fnndsc/cumin": "^3.30.6",
+    "@fnndsc/salsa": "^4.5.5",
     "bsd-trek": "^0.4.0",
     "chalk": "^4.1.2",
     "cli-highlight": "^2.1.11",

package/dist/builtins/res/pipeline.args.d.ts

@@ -1,35 +0,0 @@
-/**
- * @file Pure argument parsing for the `pipeline run` subcommand.
- *
- * Dependency-free for easy unit testing.
- *
- * @module
- */
-import type { PipelineInvocationBinding } from '@fnndsc/salsa';
-/**
- * Optional overrides parsed from `pipeline run` arguments.
- */
-export interface PipelineRunOverrides {
-    computeOverride: string | undefined;
-    previousOverride: number | undefined;
-    paramFile: string | undefined;
-    bindings: PipelineInvocationBinding[];
-    /** Whether the operator asked for the handle rather than the outcome. */
-    detach: boolean;
-    /** Whether the echo of the resolved call lists every parameter of every piping. */
-    verbose: boolean;
-    /** Whether the run is resolved and printed only (`whatif`). */
-    dry: boolean;
-    /** A dry run on a feed that would be rooted first, so no node exists to attach to. */
-    dryNewFeed: boolean;
-    parseError: string | null;
-}
-/**
- * Parses `--compute <resource>`, `--previous <inst_id>`, `--paramFile <path>`
- * `--detach`, `--verbose` and `--whatif` from `pipeline run <name|id> ...` arguments (scanning from
- * index 2). Anything else in `--node.field value` form is a binding.
- *
- * @param args - The full `pipeline run` argument list.
- * @returns The parsed overrides.
- */
-export declare function pipelineRunArgs_parse(args: string[]): PipelineRunOverrides;

package/dist/builtins/res/pipeline.args.js

@@ -1,94 +0,0 @@
-import { executableArguments_parse } from '../argumentTokens.js';
-/**
- * Parses `--compute <resource>`, `--previous <inst_id>`, `--paramFile <path>`
- * `--detach`, `--verbose` and `--whatif` from `pipeline run <name|id> ...` arguments (scanning from
- * index 2). Anything else in `--node.field value` form is a binding.
- *
- * @param args - The full `pipeline run` argument list.
- * @returns The parsed overrides.
- */
-export function pipelineRunArgs_parse(args) {
-    let computeOverride;
-    let previousOverride;
-    let paramFile;
-    const bindings = [];
-    let detach = false;
-    let verbose = false;
-    let dry = false;
-    let dryNewFeed = false;
-    let parseError = null;
-    for (let i = 2; i < args.length; i++) {
-        const token = args[i];
-        if (token === '--compute') {
-            const value = args[i + 1];
-            if (value === undefined || value.startsWith('--')) {
-                parseError = '--compute requires a resource';
-                break;
-            }
-            computeOverride = value;
-            i++;
-        }
-        else if (token === '--previous') {
-            const value = args[i + 1];
-            if (value === undefined || !/^\d+$/.test(value)) {
-                parseError = '--previous requires a positive plugin instance ID';
-                break;
-            }
-            previousOverride = Number(value);
-            i++;
-        }
-        else if (token === '--detach') {
-            detach = true;
-        }
-        else if (token === '--verbose') {
-            verbose = true;
-        }
-        else if (token === '--whatif' || token === '--whatif-new-feed') {
-            dry = true;
-            dryNewFeed ||= token === '--whatif-new-feed';
-        }
-        else if (token === '--paramFile') {
-            const value = args[i + 1];
-            if (paramFile !== undefined) {
-                parseError = '--paramFile may be supplied only once';
-                break;
-            }
-            if (value === undefined || value.startsWith('--')) {
-                parseError = '--paramFile requires a CFS path';
-                break;
-            }
-            paramFile = value;
-            i++;
-        }
-        else if (token.startsWith('--')) {
-            const option = token.slice(2);
-            const equalsIndex = option.indexOf('=');
-            const compound = equalsIndex === -1 ? option : option.slice(0, equalsIndex);
-            const separator = compound.lastIndexOf('.');
-            if (separator <= 0 || separator === compound.length - 1) {
-                parseError = `unsupported pipeline option: ${token}`;
-                break;
-            }
-            const node = compound.slice(0, separator);
-            const field = compound.slice(separator + 1);
-            let value;
-            if (equalsIndex >= 0) {
-                value = executableArguments_parse([`--${field}=${option.slice(equalsIndex + 1)}`])[field];
-            }
-            else {
-                const next = args[i + 1];
-                const consumesNext = next !== undefined && (!next.startsWith('--') || /^-\d/.test(next));
-                value = executableArguments_parse(consumesNext ? [`--${field}`, next] : [`--${field}`])[field];
-                if (consumesNext)
-                    i++;
-            }
-            bindings.push({ node, field, value });
-        }
-        else {
-            parseError = `unexpected pipeline argument: ${token}`;
-            break;
-        }
-    }
-    return { computeOverride, previousOverride, paramFile, bindings, detach, verbose, dry, dryNewFeed, parseError };
-}
-//# sourceMappingURL=pipeline.args.js.map

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package/dist/chris/help.d.ts

@@ -1,18 +0,0 @@
-/**
- * @file The ChRIS backend's help: a page for each command it registers.
- *
- * The core's own commands keep their pages in `builtins/help.ts`; these are
- * registered with the ChRIS commands, so a session without ChRIS has none.
- *
- * @module
- */
-import type { CommandHelp } from '../core/commandRegistry.js';
-/**
- * Standard subcommands and options injected into every resource help entry.
- * Captures the Resource Contract documented in CONTEXT.md.
- */
-export declare const RESOURCE_LIST_OPTIONS: string[];
-/** The help for each ChRIS command, by name. */
-/** The built-in names the ChRIS session answers, for `help variables`. */
-export declare const CHRIS_BUILTIN_LINES: ReadonlyArray<string>;
-export declare const chrisHelp: Record<string, CommandHelp>;

package/dist/chris/help.js

@@ -1,229 +0,0 @@
-/**
- * Standard subcommands and options injected into every resource help entry.
- * Captures the Resource Contract documented in CONTEXT.md.
- */
-export const RESOURCE_LIST_OPTIONS = [
-    '',
-    'STANDARD SUBCOMMANDS:',
-    '  list              List resources (default: 20 per page)',
-    '  search <term>     Search resources (alias: list --search <term>)',
-    '  inspect           List available field names',
-    '',
-    'STANDARD OPTIONS:',
-    '  --all             Fetch all pages',
-    '  --limit <n>       Page size (default: 20)',
-    '  --fields <f,f>    Columns to display',
-    '  --sort <field>    Sort by field',
-    '  --reverse         Reverse sort order',
-    '  --table           Tabular output',
-    '  --csv             CSV output',
-];
-/** The help for each ChRIS command, by name. */
-/** The built-in names the ChRIS session answers, for `help variables`. */
-export const CHRIS_BUILTIN_LINES = [
-    '  ${gather}        every gathered member, as operands (where it was gathered FROM); read live',
-    '  ${gather.series.folderPath}  the same members, where they LANDED in CUBE',
-    '  ${gather.name}  ${gather.feed.id}  any field of the cohort, as `gather` answers it',
-];
-export const chrisHelp = {
-    plugin: {
-        category: 'Resources',
-        usage: 'plugin <subcommand> [options]',
-        description: 'Work with a single ChRIS plugin - search, view documentation',
-        options: [
-            '',
-            'DESCRIPTION:',
-            '  Plugins are computational units in ChRIS that process data. The "plugin"',
-            '  command operates on individual plugins - searching for specific plugins, or',
-            '  viewing their documentation. A plugin RUNS by its name, as a line of its own,',
-            '  where the session stands: pl-dcm2niix-v1.0.2 … (A=$(…) names the run).',
-            '',
-            'SUBCOMMANDS:',
-            '  info <name>-v<version>       Show one plugin whole: facts and every parameter',
-            '  search <searchable>          Resolve a searchable to plugin IDs',
-            '  readme <pluginId>            Display plugin README documentation',
-            '  add <name|image|url>         Register a plugin: by name or image (peer store, then the image), or a plugin URL in another CUBE',
-            '  add --json <file>            Register one descriptor file (a host path; cube:<path> for one in CUBE)',
-            '  sync [source]                Fill this CUBE from a plugin index: show the plan, ask, register what is missing',
-            '  validate <file|dir|source>   Check descriptors without a CUBE (a host path; owner/repo[@ref] or cube:<path>)',
-            '  index [<owner/repo[@ref]>]   Show or set the index sync reads; --reset restores FNNDSC/chris-plugins@main',
-            '',
-            'PLUGIN SYNC:',
-            '  A source is owner/repo[@ref] (GitHub), a CUBE path (a directory of .json, or a .tar.gz), or host:<path>.',
-            '  --ref <tag|commit>  pin the index   --plan  show the plan and stop   --yes  apply without asking',
-            '  --compute a,b       register on these compute resources (default: all of them)',
-            '  Sync never deletes and never changes a plugin already there; drift and newer-in-CUBE are reported.',
-            '  Anyone may see the plan; applying it needs an administrator (sudo plugin sync).',
-            '',
-            'PLUGIN VALIDATE:',
-            '  Rules: 1 schema · 2 CUBE upload rules · 3 file name = name · 4 no case clash · 5 images resolve',
-            '  --offline           skip rule 5 (the registry lookups); the report says it was not checked',
-            '',
-            'SEARCHABLE FORMATS:',
-            '  Simple:     pl-dircopy',
-            '  Compound:   name:pl-dircopy,version:1.3.2',
-            '  ID-based:   id:42',
-            '  Batch:      id:77++id:33  (multiple plugins)',
-            '',
-            'RUNNING A PLUGIN:',
-            '  pl-dcm2niix-v1.0.2 --param value -- feed_title="T"   run where you stand',
-            '  pl-dcm2niix …                 the bare name runs the highest version, and says which',
-            '  pl-dcm2niix ~/uploads/subjects                     on that tree instead of where you stand',
-            '  pl-dcm2niix ~/uploads/t1.nii as sub-01 --param v   one subject, the file in it; operands first',
-            '  A=$(pl-dcm2niix-v1.0.2 …)                         and name the run',
-            '',
-            '  Run "parametersofplugin <name>" to see available parameters for a plugin.',
-        ],
-        examples: [
-            '# Read one plugin: the same manual "cat /bin/<entry>" prints',
-            'plugin info pl-dircopy-v1.0.0',
-            'plugin info pl-dircopy 1.0.0',
-            '',
-            '# Search for plugins',
-            'plugin search pl-dircopy',
-            'plugin search name:dcm2niix',
-            'plugin search id:42',
-            '',
-            '# View plugin documentation',
-            'plugin readme 42',
-            'plugin readme pl-dircopy',
-            '',
-            '# Register plugins',
-            'sudo plugin add pl-dircopy',
-            'sudo plugin add --json ./pl-dircopy.json',
-            'plugin sync --plan',
-            'sudo plugin sync FNNDSC/chris-plugins --ref 8c9a1f6',
-            'plugin validate ./plugins --offline',
-            '',
-            '# Run a plugin where you stand, and name the run',
-            'A=$(pl-dcm2niix-v1.0.2)',
-            'cd ${A.outputPath}',
-        ],
-    },
-    plugins: {
-        category: 'Resources',
-        usage: 'plugins <subcommand> [options]',
-        description: 'Manage collections of ChRIS plugins - list, add, delete, query',
-        options: [
-            '',
-            'DESCRIPTION:',
-            '  Plugins are computational units in ChRIS. The "plugins" command operates on',
-            '  collections of plugins - listing all available plugins, adding new plugins to',
-            '  ChRIS, deleting plugins, or querying plugin metadata.',
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  add <input>       [admin] Register a new plugin to ChRIS',
-            '  delete <id>       [admin] Remove a plugin from ChRIS',
-            '  overview          Show plugin system overview',
-            '',
-            'PLUGINS ADD OPTIONS:',
-            '  --compute <resources>         Comma-separated compute resources (default: host)',
-            '  --store <url>                 Peer store URL (default: cube.chrisproject.org)',
-            '  --adminUser <username>        Administrator username (non-interactive compatibility)',
-            '  --adminPassword <password>    Administrator password (non-interactive compatibility)',
-            '  --publicRepo <url>            Public repository URL for the plugin',
-            '',
-            'PLUGIN INPUT FORMATS:',
-            '  Plugin name:      pl-dircopy',
-            '  Docker image:     fnndsc/pl-dircopy:2.1.1',
-            '  Store URL:        https://cube.chrisproject.org/api/v1/plugins/96/',
-        ],
-        examples: [
-            '# List all plugins',
-            'plugins list',
-            'plugins list --all',
-            'plugins list --search name:dircopy',
-            'plugins list --fields name,version,dock_image',
-            'plugins search dircopy',
-            '',
-            '# Inspect available fields',
-            'plugins inspect',
-            '',
-            '# Delete a plugin',
-            'plugins delete 42',
-            '',
-            '# Show plugin system overview',
-            'plugins overview',
-            '',
-            '# Add plugin from peer store (searches cube.chrisproject.org)',
-            'plugins add pl-dircopy',
-            'plugins add pl-dircopy --compute host,gpu',
-            '',
-            '# Add a plugin with a temporary administrator identity',
-            'sudo plugins add pl-dircopy',
-            '',
-            '# Add plugin from Docker image',
-            'plugins add fnndsc/pl-dircopy:2.1.1',
-            'plugins add fnndsc/pl-dircopy:2.1.1 --compute host',
-            '',
-            '# Add plugin from custom peer store',
-            'plugins add pl-custom --store https://my-cube.org/api/v1/',
-            '',
-            '# Add plugin with specific repository',
-            'plugins add my-plugin:latest --publicRepo https://github.com/org/my-plugin',
-        ],
-    },
-    pipeline: {
-        category: 'Resources',
-        usage: 'pipeline <subcommand> [args]',
-        description: 'Manage and execute ChRIS pipelines (registered DAG workflows)',
-        options: [
-            ...RESOURCE_LIST_OPTIONS,
-            '',
-            'RESOURCE-SPECIFIC SUBCOMMANDS:',
-            '  info <name|id>        Show pipeline nodes, plugins, and topology',
-            '  manifest <name|id|slug>  Emit complete registered invocation YAML',
-            '  run <name|id>         Run a pipeline from the feed node you are in, and wait for it',
-            '  source <name|id>      Display the pipeline YAML source file',
-            '  diagram <name|id>     Draw the pipeline as a shallow tree',
-            '    --withargs          Include stored non-null plugin defaults inline',
-            '    --signalflow        Emit SignalFlow YAML instead of the shallow tree',
-            '  delete <id>           Remove a pipeline',
-            '',
-            'RUN OPTIONS:',
-            '  --detach              Return the instance ids at once, without waiting',
-            '  --compute <resource>  Override compute resource for all nodes',
-            '  --previous <inst_id>  Start from this instance (default: the feed node cwd is in)',
-            '  --paramFile <cfs-file> Apply one sparse YAML invocation overlay',
-            '  --<node>.<parameter> <value>  Override one hosted plugin parameter',
-            '  --<node>.<control> <value>    Override one node execution control',
-            '  Use --@<piping-id>.<field> when a node title is ambiguous or shell-unsafe',
-            '',
-            'PIPELINE EXECUTABLES:',
-            '  Pipelines also appear in /bin (colored magenta) and can be invoked directly.',
-            '  <PipelineName>              Run the pipeline from the feed node you are in',
-            '  <PipelineName> --nodes      Show DAG structure (alias: --parameters)',
-            '  <PipelineName> --source     Show YAML source (alias: --readme)',
-            '  <PipelineName> --manifest   Emit complete registered invocation YAML',
-            '  <PipelineName> --diagram    Draw the shallow pipeline topology',
-            '  <PipelineName> --signalflow Emit SignalFlow YAML directly',
-            '    --withargs                Include arguments with --diagram',
-            '  cat /bin/<PipelineName>     Show a fast cached executable summary',
-        ],
-        examples: [
-            'pipeline list                          # List all pipelines',
-            'pipeline list PHI                      # Filter by name',
-            'pipeline info PHI_detection            # Show nodes and topology',
-            'pipeline manifest PHI_detection        # Registered invocation YAML',
-            'pipeline run PHI_detection             # Run from the feed node you are in',
-            'pipeline run PHI_detection --compute gpu',
-            'pipeline run PHI_detection --segmentation.threshold 0.5',
-            'pipeline run PHI_detection --paramFile ~/params/run.yaml',
-            'pipeline source PHI_detection          # Show YAML source',
-            'pipeline diagram PHI_detection         # Draw the authored DAG',
-            'pipeline diagram --withargs PHI_detection',
-            'pipeline diagram --signalflow PHI_detection | signalflow -',
-            '',
-            '# Direct invocation from /bin',
-            'PHI_detection                          # Run with defaults',
-            'PHI_detection --nodes                  # Show node structure',
-            'PHI_detection --source                 # Show YAML source',
-            'PHI_detection --manifest               # Registered invocation YAML',
-            'PHI_detection --diagram                # Draw the authored DAG',
-            'PHI_detection --signalflow             # Emit SignalFlow YAML',
-            'cat /bin/PHI_detection                 # Cached executable summary',
-        ],
-    },
-};
-//# sourceMappingURL=help.js.map

package/dist/chris/help.js.map

@@ -1 +0,0 @@
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