@fnndsc/brasa 0.57.0 → 0.57.2

package/dist/chris/binDeclarations.d.ts

@@ -12,7 +12,9 @@
  * node, the node named by its title when that is unique and shell-safe and
  * always by `@<piping id>`. Beside them stand the session's own options of
  * a `/bin` line (`--detach`, `--parameters`, `--diagram`, …), which win a
- * name both claim, and the operands: the line's input paths, which glob.
+ * name both claim; a plugin line's run fields (`--title`, `--compute`,
+ * `--cpu_limit`, …), which CUBE takes beside the parameters and a parameter
+ * of the same name wins; and the operands: the line's input paths, which glob.
  *
  * A declaration is made when the session first needs it and kept, by the
  * `/bin` entry it is made for: a plugin's carries its version
@@ -82,6 +84,8 @@ export interface PluginLine {
     readonly operands: readonly string[];
     /** The plugin's parameters given, by flag name (`dir`), each its value. */
     readonly parameters: Readonly<Record<string, string | number | boolean>>;
+    /** The run's own fields given, by the field CUBE's plugin instance takes (`title`, `compute_resource_name`, `cpu_limit`). */
+    readonly run: Readonly<Record<string, string | number>>;
     /** The run's context words, after a lone `--` (`feed_title=T`). */
     readonly context: readonly string[];
     /** Return the run's handle at once rather than wait for it. */

package/dist/chris/binDeclarations.js

@@ -33,10 +33,35 @@ const PIPELINE_SESSION_OPTIONS = {
     verbose: { long: 'verbose', summary: 'Echo every parameter of every piping before the run' },
     help: { short: 'h', long: 'help', summary: 'Show this page' },
 };
-/** The execution controls every pipeline node takes, and the kind of each. */
+/**
+ * The execution controls a run takes beside its plugin's parameters, as
+ * CUBE's plugin instance names them: every pipeline node's, and a plugin
+ * line's.
+ */
 const EXECUTION_FIELDS = [
-    ['compute_resource_name', 'compute'], ['cpu_limit', 'word'], ['memory_limit', 'word'], ['gpu_limit', 'int'], ['number_of_workers', 'int'],
+    { field: 'compute_resource_name', value: { name: 'resource', kind: 'compute' }, summary: 'compute resource' },
+    { field: 'cpu_limit', value: { name: 'millicores', kind: 'cpu' }, summary: 'CPU limit (2000m, or 2000 millicores)' },
+    { field: 'memory_limit', value: { name: 'size', kind: 'memory' }, summary: 'memory limit (512Mi, 8Gi, or MiB)' },
+    { field: 'gpu_limit', value: { name: 'gpus', kind: 'int', min: 0 }, summary: 'number of GPUs' },
+    { field: 'number_of_workers', value: { name: 'workers', kind: 'int', min: 1 }, summary: 'number of workers' },
 ];
+/**
+ * The run's own fields a plugin line takes, by property: its title and its
+ * execution controls, which CUBE's plugin-instance create reads from the
+ * same request as the plugin's parameters, each by its field's name
+ * (`--title`, `--cpu_limit`). `--compute` is `--compute_resource_name` as
+ * `pipeline run` spells it; given both, `--compute_resource_name` counts. A
+ * parameter of the plugin's that claims a name wins it, and its value goes
+ * to CUBE under that name, as a parameter.
+ */
+const PLUGIN_RUN_OPTIONS = {
+    'run.title': { field: 'title', option: { long: 'title', summary: "The run's title, as its node shows it", value: { name: 'title', kind: 'word' } } },
+    'run.compute': { field: 'compute_resource_name', option: { long: 'compute', summary: 'Run on this compute resource (as --compute_resource_name)', value: { name: 'resource', kind: 'compute' } } },
+    ...Object.fromEntries(EXECUTION_FIELDS.map((control) => [
+        `run.${control.field}`,
+        { field: control.field, option: { long: control.field, summary: `The run's ${control.summary}`, value: control.value } },
+    ])),
+};
 /** A node title usable as a selector: one shell word, no dot. */
 const SELECTOR_WORD = /^[A-Za-z0-9_-]+$/;
 /**
@@ -98,7 +123,8 @@ function parameterShort_read(parameter) {
 }
 /**
  * The options of a plugin's line: the session's, then one per parameter
- * whose names the session's options leave free, by its flag's long name.
+ * whose names the session's options leave free, by its flag's long name,
+ * then the run's own fields whose names both leave free.
  *
  * @param parameters - The plugin's parameters.
  * @returns The options, by property.
@@ -128,6 +154,12 @@ function pluginOptions_make(parameters) {
         if (usableShort !== undefined)
             shorts.add(usableShort);
     }
+    // The run's own fields, where the session's options and the parameters leave the name free.
+    for (const [key, run] of Object.entries(PLUGIN_RUN_OPTIONS)) {
+        if (run.option.long !== undefined && longs.has(run.option.long))
+            continue;
+        options[key] = run.option;
+    }
     return options;
 }
 /**
@@ -153,9 +185,12 @@ export function pluginDeclaration_make(spec, handler) {
         grammar: { operands: [INPUT_OPERAND], options: pluginOptions_make(spec.parameters) },
         help: {
             summary: spec.title ?? `The CUBE plugin ${spec.name}, version ${spec.version}`,
-            description: `${spec.description ?? `Run ${spec.name} ${spec.version}, a CUBE ${spec.kind} plugin.`} A run stands where you are, or on its operands, first on the line: a directory is the input (in a feed, that node; outside one, pl-dircopy roots a new feed of it), several directories are one run each, and files are shaped into subjects, each file its own named by its stem or the files before \`as <name>\` one.${fs} After a lone --, key=value words set the run's context (feed_title). help operands gives the full rules; whatif <line> prints a run and starts nothing.`,
+            description: `${spec.description ?? `Run ${spec.name} ${spec.version}, a CUBE ${spec.kind} plugin.`} A run stands where you are, or on its operands, first on the line: a directory is the input (in a feed, that node; outside one, pl-dircopy roots a new feed of it), several directories are one run each, and files are shaped into subjects, each file its own named by its stem or the files before \`as <name>\` one.${fs} --title, --compute and the limits set the run's own fields, as CUBE names them. After a lone --, key=value words set the run's context (feed_title). help operands gives the full rules; whatif <line> prints a run and starts nothing.`,
             category: 'Resources',
-            examples: [`${name} ~/uploads/subjects`, `${name} ~/uploads/t1.nii as sub-01`, `${name} --parameters`, `${name} --readme --raw | glow -`, `${name} -- feed_title="Brain MRI"`],
+            examples: [
+                `${name} ~/uploads/subjects`, `${name} ~/uploads/t1.nii as sub-01`, `${name} ~/uploads/subjects --title "T1 run" --compute host --memory_limit 8Gi`,
+                `${name} --parameters`, `${name} --readme --raw | glow -`, `${name} -- feed_title="Brain MRI"`,
+            ],
         },
         holds: [],
         handler,
@@ -181,10 +216,10 @@ function nodeSelectors_list(manifest, node) {
  * @returns Each field's name, kind and summary.
  */
 function nodeFields_list(node) {
-    const controls = EXECUTION_FIELDS.map(([field, kind]) => ({
-        name: field,
-        value: { name: field, kind },
-        summary: `${node.title} (${node.pluginName}): its ${field.replaceAll('_', ' ')}`,
+    const controls = EXECUTION_FIELDS.map((control) => ({
+        name: control.field,
+        value: { ...control.value, name: control.field },
+        summary: `${node.title} (${node.pluginName}): its ${control.summary}`,
     }));
     const parameters = (node.parameterDefinitions ?? [])
         .filter((parameter) => parameter.name !== 'plugininstances')
@@ -268,7 +303,7 @@ function lineRecords_read(args) {
 function pluginParameters_read(options) {
     const parameters = {};
     for (const [key, value] of Object.entries(options)) {
-        if (Object.hasOwn(PLUGIN_SESSION_OPTIONS, key))
+        if (Object.hasOwn(PLUGIN_SESSION_OPTIONS, key) || Object.hasOwn(PLUGIN_RUN_OPTIONS, key))
             continue;
         if (value === false || value === undefined)
             continue;
@@ -277,6 +312,22 @@ function pluginParameters_read(options) {
     }
     return parameters;
 }
+/**
+ * The run's own fields a parsed line gave, by the field each is posted as:
+ * `--compute` first, so `--compute_resource_name` counts when both are given.
+ *
+ * @param options - The parsed options.
+ * @returns The fields.
+ */
+function pluginRun_read(options) {
+    const run = {};
+    for (const [key, option] of Object.entries(PLUGIN_RUN_OPTIONS)) {
+        const value = options[key];
+        if (typeof value === 'string' || typeof value === 'number')
+            run[option.field] = value;
+    }
+    return run;
+}
 /**
  * A plugin line, parsed: the typed reading of the line a declaration parsed.
  *
@@ -295,6 +346,7 @@ export function pluginLine_read(args, context = []) {
     return {
         operands: operands['input'] ?? [],
         parameters: pluginParameters_read(options),
+        run: pluginRun_read(options),
         context: [...context],
         detach: options['detach'] === true,
         inspect,

package/dist/chris/binDeclarations.js.map

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package/dist/chris/expectSubjects.js

@@ -83,12 +83,11 @@ async function run_read(target) {
  */
 async function pathTags_read(ask) {
     const tagName = ask.words[0];
-    const { path_physical, tagsModel_read } = await import('../builtins/res/dicom.js');
+    const { tagsModel_read } = await import('../builtins/res/dicom.js');
     const resolved = await path_resolve(ask.target ?? '');
     if (tagName === undefined)
         return { got: null, refusal: 'expect path <p> tags <TagName> <predicate> <value>' };
-    const physical = await path_physical(resolved);
-    let model = await tagsModel_read(physical);
+    let model = await tagsModel_read(resolved);
     if (!model.ok) {
         // A plugin's output is routinely nested, so a tag claim made at the
         // node's own folder looks BENEATH it before giving up: the files a run
@@ -98,7 +97,7 @@ async function pathTags_read(ask) {
                 .filter((entry) => entry.item.type === 'dir')
                 .map((entry) => `${entry.folder.replace(/\/$/, '')}/${entry.item.name}`))];
         for (const folder of folders) {
-            const beneath = await tagsModel_read(await path_physical(folder));
+            const beneath = await tagsModel_read(folder);
             if (beneath.ok) {
                 model = beneath;
                 break;

package/dist/chris/expectSubjects.js.map

@@ -1 +1 @@
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package/dist/chris/files.js

@@ -30,7 +30,8 @@ export function fileRefusal_name(filePath, notes) {
     return new FileReadRefusal(filePath, 502, last.replace(/^\[[^\]]*\]\s*\|\s*/, '').trim() || 'could not be read');
 }
 /**
- * Writes bytes to one ChRIS path through the kernel's own create.
+ * Writes bytes to one ChRIS path through the kernel's own create, where the
+ * store keeps it (`storePath_resolve`).
  *
  * A browser surface holds bytes the daemon's machine has never seen; this
  * is how they reach the store without any surface talking to CUBE.
@@ -40,10 +41,11 @@ export function fileRefusal_name(filePath, notes) {
  * @throws {Error} When the store refused the write.
  */
 async function file_write(filePath, bytes) {
-    const { path_resolve } = await import('../builtins/utils.js');
+    const { storePath_resolve } = await import('../builtins/utils.js');
     const { files_create } = await import('@fnndsc/salsa');
     const { listCache_get } = await import('@fnndsc/cumin');
-    const resolved = await path_resolve(filePath);
+    // Where the store keeps it, as every writer asks: a `/proc` job's `data` and any link on the way.
+    const resolved = await storePath_resolve(filePath);
     const written = await files_create(bytes, resolved);
     if (!written) {
         throw new Error(`cannot write ${filePath}`);

package/dist/chris/files.js.map

@@ -1 +1 @@
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package/dist/chris/kinds.d.ts

@@ -18,6 +18,16 @@ export declare const FEED_KIND: ArgumentKind;
  * comma typed.
  */
 export declare const COMPUTE_KIND: ArgumentKind;
+/**
+ * A run's CPU limit, as CUBE's plugin instance takes it: millicores, `2000m`
+ * or a bare `2000`.
+ */
+export declare const CPU_KIND: ArgumentKind;
+/**
+ * A run's memory limit, as CUBE's plugin instance takes it: `512Mi`, `8Gi`,
+ * or a bare number of MiB.
+ */
+export declare const MEMORY_KIND: ArgumentKind;
 /**
  * A PACS query, as `pull`, `pacs pull` and `pacs status` take one: its id,
  * its path under /net/pacs/queries (or a study or series inside it), or a

package/dist/chris/kinds.js

@@ -7,6 +7,7 @@
  * - ANCHOR_KIND: an anchor of this session's berth, by name.
  * - FEED_KIND: a feed, by id, feed_N or title.
  * - COMPUTE_KIND: a compute resource, by name.
+ * - CPU_KIND / MEMORY_KIND: a run's CPU and memory limits, as CUBE writes them.
  * - PACS_QUERY_KIND: a PACS query, by id, by path, or as a question.
  * - PLUGIN_KIND: a plugin, as `/bin` names a version of it.
  * - PIPELINE_KIND: a pipeline, by its name, id or `/bin` name.
@@ -86,6 +87,44 @@ export const COMPUTE_KIND = {
         return candidates_filter(names, partial);
     },
 };
+/**
+ * A limit as CUBE writes it: a whole number above nought, bare or with one
+ * of its units. Bare, it is a number (CUBE counts it in the field's own
+ * unit); with a unit, the word as typed, which CUBE converts.
+ *
+ * @param word - The word.
+ * @param units - The units CUBE takes after the number.
+ * @param reason - What the word should be, for the refusal.
+ * @returns The value, or why it is not one.
+ */
+function limit_read(word, units, reason) {
+    const found = word.match(/^(\d+)([A-Za-z]*)$/);
+    if (found === null || Number(found[1]) <= 0)
+        return { ok: false, reason };
+    if (found[2] === '')
+        return { ok: true, value: Number(found[1]) };
+    return units.includes(found[2] ?? '') ? { ok: true, value: word } : { ok: false, reason };
+}
+/**
+ * A run's CPU limit, as CUBE's plugin instance takes it: millicores, `2000m`
+ * or a bare `2000`.
+ */
+export const CPU_KIND = {
+    name: 'cpu',
+    summary: 'a CPU limit in millicores: 2000m, or 2000',
+    word_read: (word) => limit_read(word, ['m'], 'millicores: 2000m, or 2000'),
+    schema_make: () => z.union([z.number().int().positive(), z.string().regex(/^[1-9]\d*m$/)]),
+};
+/**
+ * A run's memory limit, as CUBE's plugin instance takes it: `512Mi`, `8Gi`,
+ * or a bare number of MiB.
+ */
+export const MEMORY_KIND = {
+    name: 'memory',
+    summary: 'a memory limit: 512Mi, 8Gi, or a number of MiB',
+    word_read: (word) => limit_read(word, ['Mi', 'Gi'], 'a memory size: 512Mi, 8Gi, or a number of MiB'),
+    schema_make: () => z.union([z.number().int().positive(), z.string().regex(/^[1-9]\d*(?:Mi|Gi)$/)]),
+};
 /** Where the PACS provider keeps its queries. */
 const PACS_QUERIES_ROOT = '/net/pacs/queries/';
 /** A query asked as a question, `Key:Value[,…]` or JSON, rather than named. */
@@ -181,5 +220,5 @@ export const PIPELINE_KIND = {
     },
 };
 /** Every argument kind the ChRIS backend registers. */
-export const chrisArgumentKinds = [ANCHOR_KIND, FEED_KIND, COMPUTE_KIND, PACS_QUERY_KIND, PLUGIN_KIND, PIPELINE_KIND];
+export const chrisArgumentKinds = [ANCHOR_KIND, FEED_KIND, COMPUTE_KIND, CPU_KIND, MEMORY_KIND, PACS_QUERY_KIND, PLUGIN_KIND, PIPELINE_KIND];
 //# sourceMappingURL=kinds.js.map

package/dist/chris/kinds.js.map

@@ -1 +1 @@
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