@fnndsc/brasa 0.56.1 → 0.56.3

package/dist/builtins/res/compute.d.ts

@@ -1,8 +1,72 @@
 import { CommandEnvelope } from '@fnndsc/menu';
 /**
- * Handles compute commands.
+ * `compute [[--table] [--csv] | list [--table] [--csv] | search <term> [--table] [--csv] | inspect]`: the declaration.
  *
- * @param args - Command arguments.
- * @returns An envelope carrying the compute-resource listing or fields.
+ * @example
+ * ```ts
+ * commands_register({ declarations: [computeCommand] }, 'backend');
+ * ```
+ */
+export declare const computeCommand: import("../../core/commandDeclaration.js").CommandDeclaration<{
+    readonly bare: {
+        readonly summary: "List every compute resource, as list does";
+        readonly options: {
+            readonly table: {
+                readonly long: "table";
+                readonly summary: "Tabular output";
+            };
+            readonly csv: {
+                readonly long: "csv";
+                readonly summary: "CSV output";
+            };
+        };
+    };
+    readonly subcommands: {
+        readonly list: {
+            readonly summary: "List every compute resource";
+            readonly options: {
+                readonly table: {
+                    readonly long: "table";
+                    readonly summary: "Tabular output";
+                };
+                readonly csv: {
+                    readonly long: "csv";
+                    readonly summary: "CSV output";
+                };
+            };
+        };
+        readonly search: {
+            readonly summary: "List the compute resources a term matches: field:value, or part of a name";
+            readonly operands: readonly [{
+                readonly name: "term";
+                readonly kind: "word";
+                readonly summary: "The filter, field:value, or part of a name";
+            }];
+            readonly options: {
+                readonly table: {
+                    readonly long: "table";
+                    readonly summary: "Tabular output";
+                };
+                readonly csv: {
+                    readonly long: "csv";
+                    readonly summary: "CSV output";
+                };
+            };
+        };
+        readonly inspect: {
+            readonly summary: "Name the fields a compute resource has";
+        };
+    };
+}>;
+/**
+ * `compute` over words already split: the declaration's parse and handler.
+ *
+ * @param args - The words after `compute`.
+ * @returns The answer, or the refusal of a bad line.
+ *
+ * @example
+ * ```ts
+ * await builtin_compute(['list', '--table']);
+ * ```
  */
 export declare function builtin_compute(args: string[]): Promise<CommandEnvelope>;

package/dist/builtins/res/compute.js

@@ -1,16 +1,19 @@
 /**
- * @file Builtin compute command.
+ * @file `compute` and `computes`: the compute resources registered with
+ * CUBE, where a plugin's job runs, listed, searched, and their fields named.
  *
- * Lists compute resources registered with ChRIS CUBE.
- * Subcommands:
- * - `list` — display all available compute resources
+ * CUBE answers every compute resource in one read, so the listing takes no
+ * paging; a search filters what that read answered.
  *
- * `compute` and `computes` are both registered in COMMAND_HANDLERS.
+ * Declared in one record (`computeCommand`, `computes` among its aliases).
+ *
+ * Key components:
+ * - computeCommand: the declaration, answered as `compute` and `computes`.
+ * - builtin_compute: the declaration run over words already split.
  *
  * @module
  */
 import chalk from 'chalk';
-import { commandArgs_process } from '../utils.js';
 import { computeResources_fetchList } from '@fnndsc/chili/commands/compute/list.js';
 import { computeFields_fetch } from '@fnndsc/chili/commands/compute/fields.js';
 import { computeList_render } from '@fnndsc/chili/views/compute.js';
@@ -18,42 +21,125 @@ import { table_render } from '@fnndsc/chili/screen/screen.js';
 import { errorStack } from '@fnndsc/fond';
 import { envelope_ok, envelope_error } from '@fnndsc/menu';
 import { exitCode_set } from '../../core/handlerRun.js';
+import { command_declare } from '../../core/commandDeclaration.js';
+import { declaredCommand_run } from '../../core/commandParse.js';
 /**
- * Handles compute commands.
+ * Whether a compute resource matches a search term: `field:value` matches
+ * a field holding the value, a bare word the name holding it.
  *
- * @param args - Command arguments.
- * @returns An envelope carrying the compute-resource listing or fields.
+ * @param resource - The compute resource.
+ * @param term - The term.
+ * @returns True when it matches.
  */
-export async function builtin_compute(args) {
-    const parsed = commandArgs_process(args);
-    const subcommand = parsed._[0];
-    if (!subcommand || subcommand === 'list') {
-        try {
-            const listResult = await computeResources_fetchList();
-            if (!listResult.ok) {
-                const lastError = errorStack.stack_pop();
-                exitCode_set(1);
-                return envelope_error('', undefined, `${chalk.red(lastError ? lastError.message : 'compute list failed')}\n`);
-            }
-            return envelope_ok(`${computeList_render(listResult.value.resources, { table: !!parsed.table, csv: !!parsed.csv })}\n`);
-        }
-        catch (e) {
-            const msg = e instanceof Error ? e.message : String(e);
+function computeResource_matches(resource, term) {
+    const colon = term.indexOf(':');
+    const field = colon === -1 ? 'name' : term.slice(0, colon);
+    const value = (colon === -1 ? term : term.slice(colon + 1)).toLowerCase();
+    const held = Object.entries(resource).find(([key]) => key === field)?.[1];
+    return held !== undefined && held !== null && String(held).toLowerCase().includes(value);
+}
+/**
+ * Lists the compute resources, those a term matches when one is given.
+ *
+ * @param shape - How the listing is drawn.
+ * @param term - The search term, or none for every resource.
+ * @returns The listing, or the error.
+ */
+async function computeList_answer(shape, term) {
+    try {
+        const listResult = await computeResources_fetchList();
+        if (!listResult.ok) {
+            const lastError = errorStack.stack_pop();
             exitCode_set(1);
-            return envelope_error('', undefined, `${chalk.red(`compute error: ${msg}`)}\n`);
+            return envelope_error('', undefined, `${chalk.red(lastError ? lastError.message : 'compute list failed')}\n`);
         }
+        const resources = term === undefined
+            ? listResult.value.resources
+            : listResult.value.resources.filter((resource) => computeResource_matches(resource, term));
+        return envelope_ok(`${computeList_render(resources, { table: shape.table, csv: shape.csv })}\n`);
     }
-    if (subcommand === 'inspect') {
-        const fields = await computeFields_fetch();
-        if (fields && fields.length > 0) {
-            return envelope_ok(table_render(fields.map((f) => ({ field: f })), ['field'], { title: { title: 'Compute fields', justification: 'center' } }));
-        }
-        return envelope_ok(`${chalk.gray('No fields found.')}\n`);
+    catch (e) {
+        const msg = e instanceof Error ? e.message : String(e);
+        exitCode_set(1);
+        return envelope_error('', undefined, `${chalk.red(`compute error: ${msg}`)}\n`);
+    }
+}
+/**
+ * Names the fields a compute resource has.
+ *
+ * @returns The fields' table, or that there are none.
+ */
+async function computeFields_render() {
+    const fields = await computeFields_fetch();
+    if (fields && fields.length > 0) {
+        return envelope_ok(table_render(fields.map((f) => ({ field: f })), ['field'], { title: { title: 'Compute fields', justification: 'center' } }));
     }
-    if (subcommand === 'search') {
-        return builtin_compute(['list', '--search', parsed._[1] ?? '']);
+    return envelope_ok(`${chalk.gray('No fields found.')}\n`);
+}
+/** How a compute listing may be drawn. */
+const COMPUTE_SHAPE_OPTIONS = {
+    table: { long: 'table', summary: 'Tabular output' },
+    csv: { long: 'csv', summary: 'CSV output' },
+};
+/** What a `compute` line may hold. */
+const COMPUTE_GRAMMAR = {
+    bare: { summary: 'List every compute resource, as list does', options: COMPUTE_SHAPE_OPTIONS },
+    subcommands: {
+        list: { summary: 'List every compute resource', options: COMPUTE_SHAPE_OPTIONS },
+        search: {
+            summary: 'List the compute resources a term matches: field:value, or part of a name',
+            operands: [{ name: 'term', kind: 'word', summary: 'The filter, field:value, or part of a name' }],
+            options: COMPUTE_SHAPE_OPTIONS,
+        },
+        inspect: { summary: 'Name the fields a compute resource has' },
+    },
+};
+/**
+ * Runs one `compute` line.
+ *
+ * @param args - The line, parsed.
+ * @returns The listing, the fields, or the error.
+ */
+async function compute_run(args) {
+    switch (args.subcommand) {
+        case null:
+        case 'list': return computeList_answer(args.options);
+        case 'search': return computeList_answer(args.options, args.operands.term);
+        case 'inspect': return computeFields_render();
     }
-    exitCode_set(1);
-    return envelope_error(`${chalk.red(`Unknown subcommand: ${subcommand}. Usage: compute <list|search|inspect>`)}\n`);
+}
+/**
+ * `compute [[--table] [--csv] | list [--table] [--csv] | search <term> [--table] [--csv] | inspect]`: the declaration.
+ *
+ * @example
+ * ```ts
+ * commands_register({ declarations: [computeCommand] }, 'backend');
+ * ```
+ */
+export const computeCommand = command_declare({
+    name: 'compute',
+    aliases: ['computes'],
+    grammar: COMPUTE_GRAMMAR,
+    help: {
+        summary: 'The compute resources registered with CUBE, where jobs run',
+        description: 'List the compute resources registered with CUBE, every one in a single read, as a table or CSV when asked; search keeps those a field:value, or part of a name, matches; inspect names the fields a compute resource has. compute and computes are one command. A plugin or pipeline run takes one with --compute <name>.',
+        category: 'Resources',
+        examples: ['compute list', 'compute list --table', 'compute search moc', 'compute list --csv', 'compute inspect'],
+    },
+    handler: compute_run,
+});
+/**
+ * `compute` over words already split: the declaration's parse and handler.
+ *
+ * @param args - The words after `compute`.
+ * @returns The answer, or the refusal of a bad line.
+ *
+ * @example
+ * ```ts
+ * await builtin_compute(['list', '--table']);
+ * ```
+ */
+export async function builtin_compute(args) {
+    return declaredCommand_run(computeCommand, args);
 }
 //# sourceMappingURL=compute.js.map

package/dist/builtins/res/compute.js.map

@@ -1 +1 @@
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package/dist/builtins/res/dicom.d.ts

@@ -8,10 +8,59 @@ interface TagsRenderOptions {
     filter: string | undefined;
 }
 /**
- * Handles `dcm <series|tags> ...`.
+ * `dcm <series <folder> | tags [--all] [--filter <text>] <path>>`: the declaration.
  *
- * @param args - Subcommand and its arguments.
- * @returns An envelope with the rendered text and the typed model.
+ * @example
+ * ```ts
+ * commands_register({ declarations: [dcmCommand] }, 'backend');
+ * ```
+ */
+export declare const dcmCommand: import("../../core/commandDeclaration.js").CommandDeclaration<{
+    readonly subcommands: {
+        readonly series: {
+            readonly summary: "The folder as a series (one header read, order from file names)";
+            readonly operands: readonly [{
+                readonly name: "folder";
+                readonly kind: "cfsPath";
+                readonly glob: true;
+                readonly summary: "The series folder";
+            }];
+        };
+        readonly tags: {
+            readonly summary: "Every tag of a file; constant versus varying across a folder";
+            readonly operands: readonly [{
+                readonly name: "path";
+                readonly kind: "cfsPath";
+                readonly glob: true;
+                readonly summary: "A DICOM file, or a folder of them";
+            }];
+            readonly options: {
+                readonly all: {
+                    readonly long: "all";
+                    readonly summary: "Show meta and private groups too";
+                };
+                readonly filter: {
+                    readonly long: "filter";
+                    readonly summary: "Only tags whose tag, name, value or decoding contains <text>";
+                    readonly value: {
+                        readonly name: "text";
+                        readonly kind: "word";
+                    };
+                };
+            };
+        };
+    };
+}>;
+/**
+ * `dcm` over words already split: the declaration's parse and handler.
+ *
+ * @param args - The subcommand and its words.
+ * @returns An envelope with the rendered text and the typed model, or the refusal of a bad line.
+ *
+ * @example
+ * ```ts
+ * await builtin_dcm(['series', '.']);
+ * ```
  */
 export declare function builtin_dcm(args: string[]): Promise<CommandEnvelope>;
 /**
@@ -28,10 +77,9 @@ export declare function builtin_dcm(args: string[]): Promise<CommandEnvelope>;
  * same series read fine at its PACS address, and `cd` into the folder (which
  * does follow links) made the very same command work.
  *
- * So the address is resolved before anything is read: a projection through
- * the provider that owns it, then the link walk the rest of the file
- * commands already do. A path that resolves to nothing stands as it was, so
- * a bad path still refuses by its own name.
+ * So the address is resolved before anything is read, as every reader
+ * resolves it (`storePath_resolve`). A path that resolves to nothing stands
+ * as it was, so a bad path still refuses by its own name.
  *
  * @param input - The path as the operator or a surface gave it.
  * @returns The physical path, or the input when it resolves no further.

package/dist/builtins/res/dicom.js

@@ -16,46 +16,99 @@
  * there are, and which could not be read. Long values are shortened on
  * screen and say by how much; the model carries them whole.
  *
+ * Declared in one record (`dcmCommand`): two subcommands, each a path
+ * operand that globs to one path.
+ *
  * @module
  */
 import chalk from 'chalk';
 import { commandCancellation_enable, commandCancellation_signalGet } from '../../core/cancellation.js';
 import { context_getSingle, dicomSeries_summarize, dicomFolder_list, dicomHeader_get, dicomFiles_sample, dicomTags_summarize, } from '@fnndsc/salsa';
 import { DICOM_MODEL_KINDS, DICOM_TAG_GROUPS, envelope_ok, envelope_error } from '@fnndsc/menu';
-import { commandArgs_process, path_resolve } from '../utils.js';
-import { args_checkHasHelpFlag, help_render } from '../help.js';
+import { path_resolve, storePath_resolve } from '../utils.js';
 import { exitCode_set } from '../../core/handlerRun.js';
+import { command_declare } from '../../core/commandDeclaration.js';
+import { declaredCommand_run } from '../../core/commandParse.js';
 /** The most files a folder's tags are read from before sampling evenly. */
 export const DCM_TAGS_FILE_CAP = 512;
 /** On-screen values longer than this are shortened and say so. */
 const VALUE_SCREEN_LIMIT = 64;
 /** Groups a tag listing hides unless asked with `--all`. */
 const HIDDEN_GROUPS = new Set(['meta', 'private']);
+/** What a `dcm` line may hold. */
+const DCM_GRAMMAR = {
+    subcommands: {
+        series: {
+            summary: 'The folder as a series (one header read, order from file names)',
+            operands: [{ name: 'folder', kind: 'cfsPath', glob: true, summary: 'The series folder' }],
+        },
+        tags: {
+            summary: 'Every tag of a file; constant versus varying across a folder',
+            operands: [{ name: 'path', kind: 'cfsPath', glob: true, summary: 'A DICOM file, or a folder of them' }],
+            options: {
+                all: { long: 'all', summary: 'Show meta and private groups too' },
+                filter: { long: 'filter', summary: 'Only tags whose tag, name, value or decoding contains <text>', value: { name: 'text', kind: 'word' } },
+            },
+        },
+    },
+};
 /**
- * Handles `dcm <series|tags> ...`.
+ * Runs `dcm series` or `dcm tags`.
  *
- * @param args - Subcommand and its arguments.
+ * @param args - The line, parsed.
  * @returns An envelope with the rendered text and the typed model.
  */
-export async function builtin_dcm(args) {
-    if (args_checkHasHelpFlag(args, 'dcm'))
-        return envelope_ok(help_render('dcm'));
-    const subcommand = args[0];
-    switch (subcommand) {
-        case 'series':
-            return dcmSeries_handle(args.slice(1));
-        case 'tags':
-            return dcmTags_handle(args.slice(1));
-        default:
-            return usage_error(subcommand === undefined ? 'dcm: a subcommand is required' : `dcm: unknown subcommand '${subcommand}'`);
-    }
+async function dcm_run(args) {
+    if (args.subcommand === 'series')
+        return dcmSeries_handle(args.operands.folder);
+    return dcmTags_handle(args.operands.path, { all: args.options.all, filter: args.options.filter });
 }
 /**
- * An error envelope carrying the usage line.
+ * `dcm <series <folder> | tags [--all] [--filter <text>] <path>>`: the declaration.
+ *
+ * @example
+ * ```ts
+ * commands_register({ declarations: [dcmCommand] }, 'backend');
+ * ```
  */
-function usage_error(reason) {
-    exitCode_set(1);
-    return envelope_error('', undefined, `${chalk.red(reason)}\n${chalk.gray('Usage: dcm series <folder> | dcm tags <file|folder> [--all] [--filter <text>]')}\n`);
+export const dcmCommand = command_declare({
+    name: 'dcm',
+    grammar: DCM_GRAMMAR,
+    help: {
+        summary: 'DICOM as the kernel sees it: a folder as a series, a file or folder as tags',
+        description: 'Read DICOM without leaving the session. `dcm series` answers what a folder is as a series: '
+            + 'identity, modality, instance count, stack order, geometry, transfer syntax, bytes, and any '
+            + 'annotations saved for its UID. `dcm tags` lists every element of a file, or what a folder\'s '
+            + 'files share against what changes across them. Identifying tags are marked PHI and shown; '
+            + 'a shared surface redacts them by that mark. A folder\'s tags are read from every file up to '
+            + `${DCM_TAGS_FILE_CAP}, then from an even sample; the listing says how many were read of how many there are.`,
+        category: 'Imaging',
+        examples: [
+            'dcm series .                                  # This folder as a series',
+            'dcm series /SERVICES/PACS/PACSDCM/patient/study/00005-T1-abcdef0',
+            'dcm tags 0001-1.2.840.113619.2.55.3.1.dcm      # One file, grouped by module',
+            'dcm tags . --filter Position                   # Position tags across the folder',
+            'dcm tags . --all                               # Meta and private groups included',
+        ],
+    },
+    // Reading a series' listing and header, or a file's tags, changes nothing
+    // of the session: `dcm` answers with a model.
+    holds: [],
+    handler: dcm_run,
+});
+/**
+ * `dcm` over words already split: the declaration's parse and handler.
+ *
+ * @param args - The subcommand and its words.
+ * @returns An envelope with the rendered text and the typed model, or the refusal of a bad line.
+ *
+ * @example
+ * ```ts
+ * await builtin_dcm(['series', '.']);
+ * ```
+ */
+export async function builtin_dcm(args) {
+    return declaredCommand_run(dcmCommand, args);
 }
 /**
  * The address the bytes actually live at.
@@ -71,10 +124,9 @@ function usage_error(reason) {
  * same series read fine at its PACS address, and `cd` into the folder (which
  * does follow links) made the very same command work.
  *
- * So the address is resolved before anything is read: a projection through
- * the provider that owns it, then the link walk the rest of the file
- * commands already do. A path that resolves to nothing stands as it was, so
- * a bad path still refuses by its own name.
+ * So the address is resolved before anything is read, as every reader
+ * resolves it (`storePath_resolve`). A path that resolves to nothing stands
+ * as it was, so a bad path still refuses by its own name.
  *
  * @param input - The path as the operator or a surface gave it.
  * @returns The physical path, or the input when it resolves no further.
@@ -84,20 +136,7 @@ export async function path_physical(input) {
     // dispatcher, a path no link walk knows — leaves the address as it was,
     // and the command refuses by its own name rather than by an exception.
     try {
-        const { vfsDispatcher } = await import('@fnndsc/salsa');
-        let candidate = input;
-        if (vfsDispatcher?.path_isVirtual?.(input) === true) {
-            const link = /^(\/proc\/jobs\/feed_\d+\/[^/]+\/data)(\/.*)?$/.exec(input);
-            if (link === null)
-                return input;
-            const target = await vfsDispatcher.linkTarget_resolve(link[1]);
-            if (!target.ok)
-                return input;
-            candidate = `${target.value}${link[2] ?? ''}`;
-        }
-        const { logicalPath_resolve } = await import('@fnndsc/chili/utils');
-        const physical = await logicalPath_resolve(candidate);
-        return physical.ok ? physical.value : candidate;
+        return await storePath_resolve(input);
     }
     catch {
         return input;
@@ -105,12 +144,11 @@ export async function path_physical(input) {
 }
 /**
  * `dcm series <folder>`: the folder as a series.
+ *
+ * @param target - The folder, as the line named it.
+ * @returns The series' text and model, or the refusal.
  */
-async function dcmSeries_handle(args) {
-    const parsed = commandArgs_process(args);
-    const target = parsed._[0];
-    if (target === undefined)
-        return usage_error('dcm series: a folder is required');
+async function dcmSeries_handle(target) {
     // A stop is honoured between the reads; one already on its way to CUBE
     // runs to its answer, which is then dropped.
     commandCancellation_enable();
@@ -141,16 +179,12 @@ async function annotationRoot_get() {
 }
 /**
  * `dcm tags <file|folder> [--all] [--filter <text>]`.
+ *
+ * @param target - The file or folder, as the line named it.
+ * @param options - Whether hidden groups show, and the filter.
+ * @returns The tags' text and model, or the refusal.
  */
-async function dcmTags_handle(args) {
-    const parsed = commandArgs_process(args, { booleanLongOptions: ['all'] });
-    const target = parsed._[0];
-    if (target === undefined)
-        return usage_error('dcm tags: a file or folder is required');
-    const options = {
-        all: parsed.all === true,
-        filter: typeof parsed.filter === 'string' ? parsed.filter : undefined,
-    };
+async function dcmTags_handle(target, options) {
     const resolved = await path_physical(await path_resolve(target));
     const model = await tagsModel_read(resolved);
     if (!model.ok) {

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