@fnndsc/brasa 0.56.2 → 0.56.4

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

@@ -1 +1 @@
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package/dist/builtins/net/query.args.d.ts

@@ -0,0 +1,95 @@
+/**
+ * @file What a PACS query's line may hold, as `query` and `pacs query` both
+ * take it: the question, and how its answer should read.
+ *
+ * One grammar, so the standalone verb and the subcommand cannot drift. It
+ * lives apart from the query verb so `pacs` reads it without loading that
+ * verb's graph.
+ *
+ * Key components:
+ * - QUERY_GRAMMAR: the operands and options.
+ * - QueryLine: what a handler of either line reads.
+ *
+ * Dependencies: the declaration types only.
+ *
+ * @module
+ */
+import type { CommandArguments } from '../../core/commandDeclaration.js';
+/**
+ * A PACS query's operands and options.
+ *
+ * @example
+ * ```ts
+ * const queryCommand = command_declare({ name: 'query', grammar: QUERY_GRAMMAR, help, handler });
+ * ```
+ */
+export declare const QUERY_GRAMMAR: {
+    readonly operands: readonly [{
+        readonly name: "expression";
+        readonly kind: "word";
+        readonly optional: true;
+        readonly repeat: true;
+        readonly summary: "The question: Key:Value[,Key:Value…] (Key:a,b,c asks for each), or a JSON object";
+    }];
+    readonly options: {
+        readonly title: {
+            readonly long: "title";
+            readonly summary: "Title for the query record (default: Query <timestamp>)";
+            readonly value: {
+                readonly name: "title";
+                readonly kind: "word";
+            };
+        };
+        readonly pacsserver: {
+            readonly long: "pacsserver";
+            readonly summary: "Override the PACS server (default: the context's); a comma-separated list asks each";
+            readonly value: {
+                readonly name: "id";
+                readonly kind: "word";
+            };
+        };
+        readonly patients: {
+            readonly long: "patients";
+            readonly summary: "Ask after several patients: MRNs comma-separated, or @<cfs-file> (one per line)";
+            readonly value: {
+                readonly name: "list";
+                readonly kind: "word";
+            };
+        };
+        readonly csv: {
+            readonly long: "csv";
+            readonly summary: "Render the answer as CSV (a row per study, and one per patient with none)";
+        };
+        readonly csvTo: {
+            readonly long: "csv-to";
+            readonly asks: true;
+            readonly summary: "Write that CSV into ChRIS storage; given no path, the destination is asked for";
+            readonly value: {
+                readonly name: "cfs-path";
+                readonly kind: "cfsPath";
+            };
+        };
+        readonly force: {
+            readonly long: "force";
+            readonly summary: "Overwrite the table at that path; without it, an existing file is kept";
+        };
+        readonly table: {
+            readonly long: "table";
+            readonly summary: "Show the answer's rows as an aligned table: the CSV's columns, for a screen";
+        };
+        readonly series: {
+            readonly long: "series";
+            readonly summary: "One row per series instead of per study; alone, it shows the series table";
+        };
+        readonly anon: {
+            readonly long: "anon";
+            readonly summary: "Stand in for names and record numbers (for demonstrating on a live PACS)";
+        };
+        readonly fresh: {
+            readonly long: "fresh";
+            readonly summary: "Ask the PACS even if this question was answered before";
+        };
+    };
+};
+/** What a handler of a query line reads: the question and the options, from `query` or `pacs query`. */
+export type QueryLine = Pick<CommandArguments<typeof QUERY_GRAMMAR>, 'operands' | 'options'>;

package/dist/builtins/net/query.args.js

@@ -0,0 +1,26 @@
+/**
+ * A PACS query's operands and options.
+ *
+ * @example
+ * ```ts
+ * const queryCommand = command_declare({ name: 'query', grammar: QUERY_GRAMMAR, help, handler });
+ * ```
+ */
+export const QUERY_GRAMMAR = {
+    operands: [
+        { name: 'expression', kind: 'word', optional: true, repeat: true, summary: 'The question: Key:Value[,Key:Value…] (Key:a,b,c asks for each), or a JSON object' },
+    ],
+    options: {
+        title: { long: 'title', summary: 'Title for the query record (default: Query <timestamp>)', value: { name: 'title', kind: 'word' } },
+        pacsserver: { long: 'pacsserver', summary: 'Override the PACS server (default: the context\'s); a comma-separated list asks each', value: { name: 'id', kind: 'word' } },
+        patients: { long: 'patients', summary: 'Ask after several patients: MRNs comma-separated, or @<cfs-file> (one per line)', value: { name: 'list', kind: 'word' } },
+        csv: { long: 'csv', summary: 'Render the answer as CSV (a row per study, and one per patient with none)' },
+        csvTo: { long: 'csv-to', asks: true, summary: 'Write that CSV into ChRIS storage; given no path, the destination is asked for', value: { name: 'cfs-path', kind: 'cfsPath' } },
+        force: { long: 'force', summary: 'Overwrite the table at that path; without it, an existing file is kept' },
+        table: { long: 'table', summary: 'Show the answer\'s rows as an aligned table: the CSV\'s columns, for a screen' },
+        series: { long: 'series', summary: 'One row per series instead of per study; alone, it shows the series table' },
+        anon: { long: 'anon', summary: 'Stand in for names and record numbers (for demonstrating on a live PACS)' },
+        fresh: { long: 'fresh', summary: 'Ask the PACS even if this question was answered before' },
+    },
+};
+//# sourceMappingURL=query.args.js.map

package/dist/builtins/net/query.args.js.map

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

@@ -11,6 +11,7 @@
 import { PACSQueryDecodedResult, type SeriesStorageFilter } from '@fnndsc/cumin';
 import { type PacsQueryModel, type CommandEnvelope } from '@fnndsc/menu';
 import { pacsQueryModel_build } from './query.model.js';
+import { type QueryLine } from './query.args.js';
 /**
  * Result of a successful query-create-and-wait operation.
  *
@@ -88,12 +89,104 @@ export declare function pacsIdentifier_resolve(pacsserver: string): Promise<stri
  */
 export declare function age_describe(at: string): string | null;
 /**
- * Creates a PACS query, waits for results, displays findings, and prints the VFS path.
+ * `query <Key:Value…> [options]`: the declaration. `pacs query` takes the
+ * same line (`QUERY_GRAMMAR`) and runs the same handler.
  *
- * @param args - `<queryExpression> [--title <title>] [--pacsserver <id>] [--table] [--help]`
  * @example
- * query PatientID:1234
- * query 'PatientID:1234,StudyDate:20240101' --title 'Hip DDH Jan 2024'
- * query AccessionNumber:12345678 --table
+ * ```ts
+ * commands_register({ declarations: [queryCommand] }, 'backend');
+ * ```
+ */
+export declare const queryCommand: import("../../core/commandDeclaration.js").CommandDeclaration<{
+    readonly operands: readonly [{
+        readonly name: "expression";
+        readonly kind: "word";
+        readonly optional: true;
+        readonly repeat: true;
+        readonly summary: "The question: Key:Value[,Key:Value…] (Key:a,b,c asks for each), or a JSON object";
+    }];
+    readonly options: {
+        readonly title: {
+            readonly long: "title";
+            readonly summary: "Title for the query record (default: Query <timestamp>)";
+            readonly value: {
+                readonly name: "title";
+                readonly kind: "word";
+            };
+        };
+        readonly pacsserver: {
+            readonly long: "pacsserver";
+            readonly summary: "Override the PACS server (default: the context's); a comma-separated list asks each";
+            readonly value: {
+                readonly name: "id";
+                readonly kind: "word";
+            };
+        };
+        readonly patients: {
+            readonly long: "patients";
+            readonly summary: "Ask after several patients: MRNs comma-separated, or @<cfs-file> (one per line)";
+            readonly value: {
+                readonly name: "list";
+                readonly kind: "word";
+            };
+        };
+        readonly csv: {
+            readonly long: "csv";
+            readonly summary: "Render the answer as CSV (a row per study, and one per patient with none)";
+        };
+        readonly csvTo: {
+            readonly long: "csv-to";
+            readonly asks: true;
+            readonly summary: "Write that CSV into ChRIS storage; given no path, the destination is asked for";
+            readonly value: {
+                readonly name: "cfs-path";
+                readonly kind: "cfsPath";
+            };
+        };
+        readonly force: {
+            readonly long: "force";
+            readonly summary: "Overwrite the table at that path; without it, an existing file is kept";
+        };
+        readonly table: {
+            readonly long: "table";
+            readonly summary: "Show the answer's rows as an aligned table: the CSV's columns, for a screen";
+        };
+        readonly series: {
+            readonly long: "series";
+            readonly summary: "One row per series instead of per study; alone, it shows the series table";
+        };
+        readonly anon: {
+            readonly long: "anon";
+            readonly summary: "Stand in for names and record numbers (for demonstrating on a live PACS)";
+        };
+        readonly fresh: {
+            readonly long: "fresh";
+            readonly summary: "Ask the PACS even if this question was answered before";
+        };
+    };
+}>;
+/**
+ * `query` over words already split: the declaration's parse and handler.
+ *
+ * @param args - The words after `query`.
+ * @returns The answer, or the refusal of a bad line.
+ *
+ * @example
+ * ```ts
+ * await builtin_query(['PatientID:1234', '--table']);
+ * ```
  */
 export declare function builtin_query(args: string[]): Promise<CommandEnvelope>;
+/**
+ * Creates a PACS query, waits for results, displays findings, and prints the
+ * VFS path: the handler of `query` and of `pacs query`.
+ *
+ * @param args - The line, parsed.
+ * @returns The answer, its model beside it.
+ *
+ * @example
+ * ```ts
+ * await queryLine_run({ operands: { expression: ['PatientID:1234'] }, options: { …, table: true } });
+ * ```
+ */
+export declare function queryLine_run(args: QueryLine): Promise<CommandEnvelope>;

package/dist/builtins/net/query.js

@@ -20,8 +20,10 @@ import { ignoredKeys_hint } from './query.ignored.js';
 import { csvFile_write, pacsAnswer_renderCsv, pacsAnswer_renderTable } from './query.csv.js';
 import { series_cubePathGet } from './pacsUtils.js';
 import { spinner } from '../../lib/spinner.js';
-import { args_checkHasHelpFlag, help_render } from '../help.js';
 import { pacsRefusal_hint, pacsRefusal_is } from './pacsAccess.js';
+import { QUERY_GRAMMAR } from './query.args.js';
+import { command_declare } from '../../core/commandDeclaration.js';
+import { declaredCommand_run } from '../../core/commandParse.js';
 import { errorStack } from '@fnndsc/fond';
 import { exitCode_set } from '../../core/handlerRun.js';
 const QUERY_POLL_INTERVAL_MS = 2_000;
@@ -817,92 +819,96 @@ async function cohort_answer(asks, facts) {
     return envelope_ok(rendered, { kind: PACS_QUERY_MODEL_KIND, data: model });
 }
 /**
- * Creates a PACS query, waits for results, displays findings, and prints the VFS path.
+ * `query <Key:Value…> [options]`: the declaration. `pacs query` takes the
+ * same line (`QUERY_GRAMMAR`) and runs the same handler.
  *
- * @param args - `<queryExpression> [--title <title>] [--pacsserver <id>] [--table] [--help]`
  * @example
- * query PatientID:1234
- * query 'PatientID:1234,StudyDate:20240101' --title 'Hip DDH Jan 2024'
- * query AccessionNumber:12345678 --table
+ * ```ts
+ * commands_register({ declarations: [queryCommand] }, 'backend');
+ * ```
+ */
+export const queryCommand = command_declare({
+    name: 'query',
+    grammar: QUERY_GRAMMAR,
+    help: {
+        summary: 'Create a PACS query, wait for results, and print the VFS path',
+        description: 'Create a PACS query, wait for its answer, show it, and print the VFS path a pull or a cd takes. '
+            + 'A question already answered is replayed from the index, its age said; --fresh asks again. '
+            + 'A PACS matches one patient at a time, so several MRNs (PatientID:1,2,3 or --patients) is several queries, one table. '
+            + 'Some PACS ignore keys: PACSDCM answers SeriesDescription and StudyDescription as if they were not asked (query says so); '
+            + 'narrow the answer with grep. The keys each server ignores are in ~/.config/mise/pacs.json, as '
+            + '{"ignoredKeys": {"PACSDCM": ["SeriesDescription", "StudyDescription"]}}.',
+        category: 'PACS',
+        examples: [
+            'query PatientID:1234',
+            'query PatientID:1234 --fresh           # ignore the stored answer',
+            'query AccessionNumber:12345678 --title "Hip DDH workup"',
+            'query PatientID:1234,StudyDate:20240101',
+            'query PatientID:1234567,Modality:MR | grep -i t1 | grep -vi gadavist',
+            '',
+            '# A PACS matches one patient at a time, so several MRNs is several queries',
+            'query PatientID:1234,4532,6654         # three questions, one table',
+            'query --patients @~/cohorts/ddh.txt    # a cohort from a file in ChRIS',
+            'query StudyDate:20240101 --patients 1234,4532   # narrowed, per patient',
+            'query PatientID:1234 --pacsserver PACSDCM,ORTHANC   # ask both, one listing',
+            '',
+            '# A cohort audit, as a table a spreadsheet reads',
+            'query --patients @~/cohorts/ddh.txt --csv > audit.csv    # a local terminal',
+            'query --patients @~/cohorts/ddh.txt --csv-to ~/audits/ddh.csv   # any surface',
+            'query PatientID:1234 --csv-to ~/audit.csv --table --series',
+            '',
+            '# Use output path directly with pull',
+            'pull $(query PatientID:1234 | grep "VFS path" | awk \'{print $3}\')',
+        ],
+    },
+    handler: queryLine_run,
+});
+/**
+ * `query` over words already split: the declaration's parse and handler.
+ *
+ * @param args - The words after `query`.
+ * @returns The answer, or the refusal of a bad line.
+ *
+ * @example
+ * ```ts
+ * await builtin_query(['PatientID:1234', '--table']);
+ * ```
  */
 export async function builtin_query(args) {
-    if (args_checkHasHelpFlag(args, 'query')) {
-        return envelope_ok(help_render('query'));
-    }
-    let title = `Query ${Date.now()}`;
-    let pacsserverOverride = null;
-    let tableMode = false;
-    let fresh = false;
-    let patientsArg = null;
-    let csv = false;
-    let csvTo = null;
-    /** True when `--csv-to` was given no value: the destination is asked for. */
-    let csvToAsk = false;
-    /** True when the operator said to overwrite a table that already exists. */
-    let force = false;
-    /**
-     * True to stand in for what the answer says about a person.
-     *
-     * For demonstrating against a live hospital PACS, where every answer
-     * carries somebody's name and record number onto the screen.
-     */
-    let anon = false;
-    /** One row per study (the default), or per series (`--series`). */
-    let level = 'study';
-    const positional = [];
-    for (let i = 0; i < args.length; i++) {
-        if (args[i] === '--title' && i + 1 < args.length) {
-            title = args[++i];
-        }
-        else if (args[i] === '--pacsserver' && i + 1 < args.length) {
-            pacsserverOverride = args[++i];
-        }
-        else if (args[i] === '--table') {
-            tableMode = true;
-        }
-        else if (args[i] === '--patients' && i + 1 < args.length) {
-            patientsArg = args[++i];
-        }
-        else if (args[i] === '--csv') {
-            csv = true;
-        }
-        else if (args[i] === '--csv-to') {
-            // A value-taking flag given no value is an ASK. `--csv-to` with
-            // nothing after it means "ask me where", which is how a graphical
-            // surface opens its errand and how a terminal gets a prompt. Given
-            // nothing and treated as nothing — which is what happened before —
-            // the operator asked for a CSV and silently got none.
-            const value = args[i + 1];
-            if (value !== undefined && !value.startsWith('--')) {
-                csvTo = args[++i];
-            }
-            else {
-                csvToAsk = true;
-            }
-        }
-        else if (args[i] === '--force') {
-            force = true;
-        }
-        else if (args[i] === '--fresh') {
-            fresh = true;
-        }
-        else if (args[i] === '--anon') {
-            anon = true;
-        }
-        else if (args[i] === '--series') {
-            level = 'series';
-        }
-        else if (args[i].startsWith('--')) {
-            // A flag this command does not know is refused by name. Dropped in
-            // silence, `--series` on a build without it answered at the study
-            // level and looked like it had been heard.
-            exitCode_set(1);
-            return envelope_error('', undefined, `${chalk.red(`query: unknown flag ${args[i]} (see pacs query --help)`)}\n`);
-        }
-        else {
-            positional.push(args[i]);
-        }
-    }
+    return declaredCommand_run(queryCommand, args);
+}
+/**
+ * Creates a PACS query, waits for results, displays findings, and prints the
+ * VFS path: the handler of `query` and of `pacs query`.
+ *
+ * @param args - The line, parsed.
+ * @returns The answer, its model beside it.
+ *
+ * @example
+ * ```ts
+ * await queryLine_run({ operands: { expression: ['PatientID:1234'] }, options: { …, table: true } });
+ * ```
+ */
+export async function queryLine_run(args) {
+    const { options } = args;
+    const title = options.title ?? `Query ${Date.now()}`;
+    const pacsserverOverride = options.pacsserver ?? null;
+    let tableMode = options.table;
+    const fresh = options.fresh;
+    const patientsArg = options.patients ?? null;
+    const csv = options.csv;
+    // A value-taking flag given no value is an ASK: `--csv-to` with nothing
+    // after it means "ask me where", which is how a graphical surface opens
+    // its errand and how a terminal gets a prompt.
+    const csvTo = options.csvTo ?? null;
+    const csvToAsk = options.csvTo === null;
+    const force = options.force;
+    // Standing in for what the answer says about a person is for
+    // demonstrating against a live hospital PACS, where every answer carries
+    // somebody's name and record number onto the screen.
+    const anon = options.anon;
+    const level = options.series ? 'series' : 'study';
+    const positional = args.operands.expression;
     // Two renderings for one screen: CSV is the answer's text, the table is
     // its rows aligned. Asked for both, neither is guessed; writing the CSV
     // to a file (`--csv-to`) leaves the screen free for the table.