@eagleoutice/flowr 2.6.1 → 2.6.2

package/benchmark/stopwatch.js

@@ -29,9 +29,9 @@ class Stopwatch {
 class Measurements {
     measurements = new Map();
     /**
-   * Start a timer for the given key, and guards that this is the first time this key is started.
-   * Call {@link IStoppableStopwatch#stop} on the returned stopwatch to stop the timer.
-   */
+     * Start a timer for the given key, and guards that this is the first time this key is started.
+     * Call {@link IStoppableStopwatch#stop} on the returned stopwatch to stop the timer.
+     */
     start(key) {
         // we guard *before* starting so there is no additional time penalty
         (0, assert_1.guard)(!this.measurements.has(key), `already started stop watch for ${JSON.stringify(key)}`);
@@ -41,9 +41,9 @@ class Measurements {
         return stopwatch;
     }
     /**
-   * Automatically call {@link Measurements#start | start} and the corresponding stop to measure the execution time of the given function.
-   * @see {@link measureAsync}
-   */
+     * Automatically call {@link Measurements#start | start} and the corresponding stop to measure the execution time of the given function.
+     * @see {@link measureAsync}
+     */
     measure(key, fn) {
         const stopwatch = this.start(key);
         const result = fn();
@@ -51,13 +51,11 @@ class Measurements {
         return result;
     }
     /**
-   * Similar to {@link measure}, but await the promise as part of the measurement
-   *
+     * Similar to {@link measure}, but await the promise as part of the measurement
      * @param key - The key to write the resulting measurement to
      * @param fn  - The function to measure
-     *
-   * @see measure
-   */
+     * @see measure
+     */
     async measureAsync(key, fn) {
         const stopwatch = this.start(key);
         const result = await fn();
@@ -65,8 +63,8 @@ class Measurements {
         return result;
     }
     /**
-   * Retrieve all measure-results, requires that all stop-watches that have been started have also been stopped.
-   */
+     * Retrieve all measure-results, requires that all stop-watches that have been started have also been stopped.
+     */
     get() {
         const result = new Map();
         for (const [key, stopwatch] of this.measurements) {

package/benchmark/summarizer/first-phase/input.d.ts

@@ -1,2 +1,8 @@
+/**
+ * Processes a single run measurement line from the benchmark output.
+ */
 export declare function processRunMeasurement(line: Buffer, fileNum: number, lineNum: number, textOutputAppendPath: string, rawOutputPath: string): Promise<void>;
+/**
+ * Processes multiple summarized run measurement files and appends an overall summary to the given path.
+ */
 export declare function processSummarizedRunMeasurement(runNum: number, summarizedFiles: string[], appendPath: string): void;

package/benchmark/summarizer/first-phase/input.js

@@ -12,6 +12,9 @@ const assert_1 = require("../../../util/assert");
 const ansi_1 = require("../../../util/text/ansi");
 const json_1 = require("../../../util/json");
 const print_1 = require("../../stats/print");
+/**
+ * Processes a single run measurement line from the benchmark output.
+ */
 async function processRunMeasurement(line, fileNum, lineNum, textOutputAppendPath, rawOutputPath) {
     let got = JSON.parse(line.toString());
     console.log(`[file ${fileNum}, line ${lineNum}] Summarize for ${got.filename}`);
@@ -54,6 +57,9 @@ async function processRunMeasurement(line, fileNum, lineNum, textOutputAppendPat
     console.log(`    - Append textual summary to ${textOutputAppendPath}`);
     fs_1.default.appendFileSync(textOutputAppendPath, `${(0, print_1.stats2string)(summarized)}\n`);
 }
+/**
+ * Processes multiple summarized run measurement files and appends an overall summary to the given path.
+ */
 function processSummarizedRunMeasurement(runNum, summarizedFiles, appendPath) {
     console.log(`Summarizing all file statistics for run ${runNum}`);
     const summaries = [];

package/benchmark/summarizer/first-phase/process.d.ts

@@ -1,5 +1,5 @@
 import type { Reduction, SummarizedSlicerStats, TimePerToken } from '../data';
-import type { SummarizedMeasurement } from '../../../util/summarizer';
+import { type SummarizedMeasurement } from '../../../util/summarizer';
 import type { PerSliceStats, SlicerStats } from '../../stats/stats';
 import type { SlicingCriteria } from '../../../slicing/criterion/parse';
 import type { RShellEngineConfig } from '../../../config';
@@ -8,7 +8,19 @@ import type { RShellEngineConfig } from '../../../config';
  * @see Slicer
  */
 export declare function summarizeSlicerStats(stats: SlicerStats, report?: (criteria: SlicingCriteria, stats: PerSliceStats) => void, engineConf?: RShellEngineConfig): Promise<Readonly<SummarizedSlicerStats>>;
+/**
+ * Summarizes the given measurements by calculating the min, max, median, mean, standard deviation, and total.
+ */
 export declare function summarizeSummarizedMeasurement(data: SummarizedMeasurement[]): SummarizedMeasurement;
+/**
+ * Summarizes the given reductions of summarized measurements.
+ */
 export declare function summarizeSummarizedReductions(reductions: Reduction<SummarizedMeasurement>[]): Reduction<SummarizedMeasurement>;
+/**
+ * Summarizes the given times per token by calculating the min, max, median, mean, and standard deviation for each measurement.
+ */
 export declare function summarizeSummarizedTimePerToken(times: TimePerToken[]): TimePerToken;
+/**
+ * Summarizes the given times per token by calculating the min, max, median, mean, and standard deviation for each measurement.
+ */
 export declare function summarizeTimePerToken(times: TimePerToken<number>[]): TimePerToken;

package/benchmark/summarizer/first-phase/process.js

@@ -299,6 +299,9 @@ function summarizePerOperationStats(nodeStats) {
     }
     return perOperationNumber;
 }
+/**
+ * Summarizes the given measurements by calculating the min, max, median, mean, standard deviation, and total.
+ */
 function summarizeSummarizedMeasurement(data) {
     data = data.filter(assert_1.isNotUndefined);
     const min = Math.min(...data.map(d => d.min).filter(assert_1.isNotUndefined));
@@ -312,6 +315,9 @@ function summarizeSummarizedMeasurement(data) {
     const total = (0, arrays_1.arraySum)(data.map(d => d.total).filter(assert_1.isNotUndefined));
     return { min, max, median, mean, std, total };
 }
+/**
+ * Summarizes the given reductions of summarized measurements.
+ */
 function summarizeSummarizedReductions(reductions) {
     return {
         numberOfDataflowNodes: summarizeSummarizedMeasurement(reductions.map(r => r.numberOfDataflowNodes)),
@@ -334,12 +340,18 @@ function summarizeReductions(reductions) {
         numberOfDataflowNodes: (0, summarizer_1.summarizeMeasurement)(reductions.map(r => r.numberOfDataflowNodes).filter(assert_1.isNotUndefined))
     };
 }
+/**
+ * Summarizes the given times per token by calculating the min, max, median, mean, and standard deviation for each measurement.
+ */
 function summarizeSummarizedTimePerToken(times) {
     return {
         raw: summarizeSummarizedMeasurement(times.map(t => t.raw)),
         normalized: summarizeSummarizedMeasurement(times.map(t => t.normalized)),
     };
 }
+/**
+ * Summarizes the given times per token by calculating the min, max, median, mean, and standard deviation for each measurement.
+ */
 function summarizeTimePerToken(times) {
     return {
         raw: (0, summarizer_1.summarizeMeasurement)(times.map(t => t.raw)),

package/benchmark/summarizer/second-phase/graph.d.ts

@@ -1,2 +1,5 @@
 import type { UltimateSlicerStats } from '../data';
+/**
+ *
+ */
 export declare function writeGraphOutput(ultimate: UltimateSlicerStats, outputGraphPath: string): void;

package/benchmark/summarizer/second-phase/graph.js

@@ -6,6 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.writeGraphOutput = writeGraphOutput;
 const fs_1 = __importDefault(require("fs"));
 const json_1 = require("../../../util/json");
+/**
+ *
+ */
 function writeGraphOutput(ultimate, outputGraphPath) {
     console.log(`Producing benchmark graph data (${outputGraphPath})...`);
     const data = [];

package/benchmark/summarizer/second-phase/process.d.ts

@@ -1,5 +1,17 @@
 import type { SummarizedSlicerStats, UltimateSlicerStats } from '../data';
+/**
+ * This big function summarizes multiple summarized stats into one ultimate stat.
+ */
 export declare function summarizeAllSummarizedStats(stats: SummarizedSlicerStats[]): UltimateSlicerStats;
+/**
+ * This big function summarizes multiple ultimate stats into one.
+ */
 export declare function summarizeAllUltimateStats(stats: UltimateSlicerStats[]): UltimateSlicerStats;
+/**
+ * Processes the next summary line.
+ */
 export declare function processNextSummary(line: Buffer, allSummarized: SummarizedSlicerStats[]): void;
+/**
+ * Processes the next ultimate summary line.
+ */
 export declare function processNextUltimateSummary(line: Buffer, allSummarized: UltimateSlicerStats[]): void;

package/benchmark/summarizer/second-phase/process.js

@@ -11,6 +11,9 @@ const assert_1 = require("../../../util/assert");
 const stats_1 = require("../../stats/stats");
 const semantics_1 = require("../../../abstract-interpretation/data-frame/semantics");
 const arrays_1 = require("../../../util/collections/arrays");
+/**
+ * This big function summarizes multiple summarized stats into one ultimate stat.
+ */
 function summarizeAllSummarizedStats(stats) {
     const commonMeasurements = new defaultmap_1.DefaultMap(() => []);
     const perSliceMeasurements = new defaultmap_1.DefaultMap(() => []);
@@ -144,6 +147,9 @@ function summarizeAllSummarizedStats(stats) {
         } : undefined
     };
 }
+/**
+ * This big function summarizes multiple ultimate stats into one.
+ */
 function summarizeAllUltimateStats(stats) {
     return {
         // these should be deterministic, so we don't technically need to use max, but we do just in case something unexpected happens :)
@@ -225,6 +231,9 @@ function summarizeAllUltimateStats(stats) {
         } : undefined
     };
 }
+/**
+ * Processes the next summary line.
+ */
 function processNextSummary(line, allSummarized) {
     let got = JSON.parse(line.toString());
     got = {
@@ -251,6 +260,9 @@ function processNextSummary(line, allSummarized) {
     };
     allSummarized.push(got.summarize);
 }
+/**
+ * Processes the next ultimate summary line.
+ */
 function processNextUltimateSummary(line, allSummarized) {
     let got = JSON.parse(line.toString());
     got = {

package/benchmark/summarizer/summarizer.d.ts

@@ -3,8 +3,7 @@
  * @module
  */
 import type { UltimateSlicerStats } from './data';
-import type { CommonSummarizerConfiguration } from '../../util/summarizer';
-import { Summarizer } from '../../util/summarizer';
+import { type CommonSummarizerConfiguration, Summarizer } from '../../util/summarizer';
 export interface BenchmarkSummarizerConfiguration extends CommonSummarizerConfiguration {
     /**
      * If given, produce graph data output (e.g., for the benchmark visualization) to the given path

package/cli/benchmark-app.js

@@ -90,7 +90,6 @@ async function benchmark() {
 }
 /**
  * Collect all R files from the given paths.
- *
  * @param files - list of files to append to
  * @param paths - list of paths to search for R files
  * @param getBaseDir - function to get the base directory of a path
@@ -104,7 +103,6 @@ async function collectFiles(files, paths, getBaseDir) {
 }
 /**
  * Find the common base directory of a list of paths.
- *
  * @param paths - list of paths
  * @returns the common base directory
  */

package/cli/common/features.d.ts

@@ -1,3 +1,9 @@
-import type { FeatureKey } from '../../statistics/features/feature';
+import { type FeatureKey } from '../../statistics/features/feature';
+/**
+ * Validate that the given features are known by flowR.
+ */
 export declare function validateFeatures(features: (string[] | ['all'] | FeatureKey[])): Set<FeatureKey>;
+/**
+ * Retrieve the archive name for the given path.
+ */
 export declare function retrieveArchiveName(p: string): string;

package/cli/common/features.js

@@ -7,6 +7,9 @@ exports.validateFeatures = validateFeatures;
 exports.retrieveArchiveName = retrieveArchiveName;
 const path_1 = __importDefault(require("path"));
 const feature_1 = require("../../statistics/features/feature");
+/**
+ * Validate that the given features are known by flowR.
+ */
 function validateFeatures(features) {
     for (const feature of features) {
         if (feature === 'all') {
@@ -22,6 +25,9 @@ function validateFeatures(features) {
     }
     return features[0] === 'all' ? feature_1.allFeatureNames : new Set(features);
 }
+/**
+ * Retrieve the archive name for the given path.
+ */
 function retrieveArchiveName(p) {
     const basepath = path_1.default.normalize(p);
     return `${basepath.endsWith(path_1.default.sep) ? basepath.substring(0, basepath.length - 1) : basepath}.tar.gz`;

package/cli/common/script.d.ts

@@ -1,6 +1,5 @@
 /**
  * The goal of this module is simply to streamline the creation of new scripts.
- *
  * @module
  */
 import { scripts } from './scripts-info';
@@ -18,4 +17,7 @@ export interface HelpContent {
  * Additionally, you can pass usage examples that may make use of the formatting instructions `{italic x}` and `{bold x}`.
  */
 export declare function helpForOptions(script: keyof typeof scripts, content: HelpContent): string;
+/**
+ * Processes the command line arguments for a given script.
+ */
 export declare function processCommandLineArgs<T extends CommonOptions>(script: keyof typeof scripts, requireAdditionally: (keyof T)[], help: HelpContent): T;

package/cli/common/script.js

@@ -7,7 +7,6 @@ exports.helpForOptions = helpForOptions;
 exports.processCommandLineArgs = processCommandLineArgs;
 /**
  * The goal of this module is simply to streamline the creation of new scripts.
- *
  * @module
  */
 const scripts_info_1 = require("./scripts-info");
@@ -35,6 +34,9 @@ function helpForOptions(script, content) {
         }
     ]);
 }
+/**
+ * Processes the command line arguments for a given script.
+ */
 function processCommandLineArgs(script, requireAdditionally, help) {
     const options = (0, command_line_args_1.default)(scripts_info_1.scripts[script].options);
     if (options.help) {

package/cli/common/scripts-info.d.ts

@@ -1,6 +1,5 @@
 /**
  * This file contains the references to all scripts, as well as their explanations and arguments.
- *
  * @module
  */
 import type { OptionDefinition } from 'command-line-usage';
@@ -89,5 +88,8 @@ declare const _scripts: {
     };
 };
 export declare const scripts: Record<keyof typeof _scripts, ScriptInformation>;
+/**
+ * Given a set of option definitions and previously provided arguments, determine which options can still be added.
+ */
 export declare function getValidOptionsForCompletion(options: readonly OptionDefinition[], prevArgs: readonly string[]): string[];
 export {};

package/cli/common/scripts-info.js

@@ -68,6 +68,9 @@ const _scripts = {
     }
 };
 exports.scripts = _scripts;
+/**
+ * Given a set of option definitions and previously provided arguments, determine which options can still be added.
+ */
 function getValidOptionsForCompletion(options, prevArgs) {
     return options.filter(o => canAddOption(o, prevArgs)).flatMap(o => {
         const args = [(0, repl_commands_1.asOptionName)(o.name)];

package/cli/flowr-main-options.d.ts

@@ -1,4 +1,7 @@
 import type { OptionDefinition } from 'command-line-usage';
+/**
+ * Returns a comma-separated list of all available master scripts.
+ */
 export declare function getScriptsText(): string;
 export declare const flowrMainOptionDefinitions: OptionDefinition[];
 export declare const defaultConfigFile = "flowr.json";

package/cli/flowr-main-options.js

@@ -4,6 +4,9 @@ exports.defaultConfigFile = exports.flowrMainOptionDefinitions = void 0;
 exports.getScriptsText = getScriptsText;
 const scripts_info_1 = require("./common/scripts-info");
 let _scriptsText;
+/**
+ * Returns a comma-separated list of all available master scripts.
+ */
 function getScriptsText() {
     if (_scriptsText === undefined) {
         _scriptsText = Array.from(Object.entries(scripts_info_1.scripts).filter(([, { type }]) => type === 'master script'), ([k]) => k).join(', ');

package/cli/repl/commands/repl-commands.d.ts

@@ -1,5 +1,8 @@
 import type { ReplCodeCommand, ReplCommand } from './repl-main';
 export declare const helpCommand: ReplCommand;
+/**
+ * Retrieve all REPL commands (including those generated from master scripts)
+ */
 export declare function getReplCommands(): Record<string, ReplCommand | ReplCodeCommand>;
 /**
  * The names of all commands including their aliases (but without the leading `:`)
@@ -10,6 +13,16 @@ export declare function getCommandNames(): string[];
  * @param command - The name of the command (without the leading `:`)
  */
 export declare function getCommand(command: string): ReplCodeCommand | ReplCommand | undefined;
+/**
+ * Formats the given argument name as a command line option (with single or double dashes).
+ */
 export declare function asOptionName(argument: string): string;
+/**
+ * Retrieve the length of the longest command name (including star and brackets if applicable)
+ */
 export declare function longestCommandName(): number;
+/**
+ * Pad the given command string to the length of the longest command name plus two spaces.
+ * @see {@link longestCommandName}
+ */
 export declare function padCmd<T>(string: T): string;

package/cli/repl/commands/repl-commands.js

@@ -20,7 +20,6 @@ const ansi_1 = require("../../../util/text/ansi");
 const args_1 = require("../../../util/text/args");
 const assert_1 = require("../../../util/assert");
 const scripts_info_1 = require("../../common/scripts-info");
-const repl_lineage_1 = require("./repl-lineage");
 const repl_query_1 = require("./repl-query");
 function printHelpForScript(script, f, starredVersion) {
     let base = `  ${(0, ansi_1.bold)(padCmd(':' + script[0] + (starredVersion ? '[*]' : '')), f)}${script[1].description}`;
@@ -88,7 +87,6 @@ const _commands = {
     'controlflow*': repl_cfg_1.controlflowStarCommand,
     'controlflowbb': repl_cfg_1.controlflowBbCommand,
     'controlflowbb*': repl_cfg_1.controlflowBbStarCommand,
-    'lineage': repl_lineage_1.lineageCommand,
     'query': repl_query_1.queryCommand,
     'query*': repl_query_1.queryStarCommand
 };
@@ -102,6 +100,9 @@ function hasModule(path) {
         return false;
     }
 }
+/**
+ * Retrieve all REPL commands (including those generated from master scripts)
+ */
 function getReplCommands() {
     if (commandsInitialized) {
         return _commands;
@@ -168,6 +169,9 @@ function getCommand(command) {
     }
     return getReplCommands()[commandMapping[command]];
 }
+/**
+ * Formats the given argument name as a command line option (with single or double dashes).
+ */
 function asOptionName(argument) {
     if (argument.length == 1) {
         return `-${argument}`;
@@ -177,12 +181,19 @@ function asOptionName(argument) {
     }
 }
 let _longestCommandName = undefined;
+/**
+ * Retrieve the length of the longest command name (including star and brackets if applicable)
+ */
 function longestCommandName() {
     if (_longestCommandName === undefined) {
         _longestCommandName = Array.from(Object.keys(getReplCommands()), k => k.endsWith('*') ? k.length + 3 : k.length).reduce((p, n) => Math.max(p, n), 0);
     }
     return _longestCommandName;
 }
+/**
+ * Pad the given command string to the length of the longest command name plus two spaces.
+ * @see {@link longestCommandName}
+ */
 function padCmd(string) {
     return String(string).padEnd(longestCommandName() + 2, ' ');
 }

package/cli/repl/commands/repl-execute.d.ts

@@ -1,3 +1,7 @@
 import type { ReplCommand, ReplCommandInformation } from './repl-main';
+/**
+ * Tries to execute the given R shell command.
+ * If not allowed, an error message is printed to the output.
+ */
 export declare function tryExecuteRShellCommand({ output, analyzer, allowRSessionAccess, remainingLine }: ReplCommandInformation): Promise<void>;
 export declare const executeCommand: ReplCommand;

package/cli/repl/commands/repl-execute.js

@@ -3,8 +3,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.executeCommand = void 0;
 exports.tryExecuteRShellCommand = tryExecuteRShellCommand;
 const ansi_1 = require("../../../util/text/ansi");
+/**
+ * Tries to execute the given R shell command.
+ * If not allowed, an error message is printed to the output.
+ */
 async function tryExecuteRShellCommand({ output, analyzer, allowRSessionAccess, remainingLine }) {
-    const parserInfo = await analyzer.parserInformation();
+    const parserInfo = analyzer.parserInformation();
     if (!allowRSessionAccess) {
         output.stderr(`${output.formatter.format('You are not allowed to execute arbitrary R code.', { style: 1 /* FontStyles.Bold */, color: 1 /* Colors.Red */, effect: ansi_1.ColorEffect.Foreground })} 
 If you want to do so, please restart flowR with the ${output.formatter.format('--r-session-access', { style: 1 /* FontStyles.Bold */ })} flag${parserInfo.name !== 'r-shell' ? '. Additionally, please enable the r-shell engine, e.g., with ' + output.formatter.format('--default-engine r-shell', { style: 1 /* FontStyles.Bold */ }) : ''}. Please be careful of the security implications of this action. When running flowR with npm, you have to use an extra ${output.formatter.format('--', { style: 1 /* FontStyles.Bold */ })} to separate flowR from npm arguments.`);
@@ -18,7 +22,7 @@ If you want to do so, please restart flowR with the ${output.formatter.format('-
 }
 async function executeRShellCommand(output, analyzer, statement) {
     try {
-        const result = await analyzer.sendCommandWithOutput(statement, {
+        const result = await analyzer.parserInformation().sendCommandWithOutput(statement, {
             from: 'both',
             automaticallyTrimOutput: true
         });

package/cli/repl/commands/repl-main.d.ts

@@ -1,11 +1,10 @@
-import type { OutputFormatter } from '../../../util/text/ansi';
-import type { FlowrAnalysisProvider } from '../../../project/flowr-analyzer';
+import { type OutputFormatter } from '../../../util/text/ansi';
+import type { FlowrAnalysisProvider, ReadonlyFlowrAnalysisProvider } from '../../../project/flowr-analyzer';
 /**
  * Defines the main interface for output of the repl.
  * This allows us to redirect it (e.g., in the case of a server connection or tests).
  *
  * The formatter allows to dynamically change the use of ansi escape sequences (see {@link OutputFormatter})
- *
  * @see standardReplOutput
  */
 export interface ReplOutput {
@@ -24,7 +23,7 @@ export declare const standardReplOutput: ReplOutput;
 export interface ReplCommandInformation {
     output: ReplOutput;
     allowRSessionAccess: boolean;
-    analyzer: FlowrAnalysisProvider;
+    analyzer: ReadonlyFlowrAnalysisProvider;
     remainingLine: string;
 }
 /**
@@ -58,6 +57,14 @@ export interface ReplCommand extends ReplBaseCommand {
      */
     fn: (info: ReplCommandInformation) => Promise<void> | void;
 }
+/**
+ * Result of parsing a REPL code command line.
+ * `rCode` may be undefined, in which case the R code of a previous REPL command will be re-used.
+ */
+interface ParsedReplLine {
+    rCode: string | undefined;
+    remaining: string[];
+}
 /**
  * Repl command that uses the {@link FlowrAnalyzer}
  */
@@ -69,10 +76,9 @@ export interface ReplCodeCommand extends ReplBaseCommand {
      */
     fn: (info: ReplCodeCommandInformation) => Promise<void> | void;
     /**
-     * Argument parser function which handles the input given after the repl command
+     * Argument parser function which handles the input given after the repl command.
+     * If no R code is returned, the input R code of a previous REPL command will be re-used for processing the current REPL command.
      */
-    argsParser: (remainingLine: string) => {
-        input: string | undefined;
-        remaining: string[];
-    };
+    argsParser: (remainingLine: string) => ParsedReplLine;
 }
+export {};

package/cli/repl/commands/repl-parse.js

@@ -133,13 +133,13 @@ exports.parseCommand = {
     argsParser: (line) => {
         return {
             // Threat the whole input line as R code
-            input: (0, retriever_1.removeRQuotes)(line.trim()),
+            rCode: (0, retriever_1.removeRQuotes)(line.trim()),
             remaining: []
         };
     },
     fn: async ({ output, analyzer }) => {
         const result = await analyzer.parse();
-        const parserInfo = await analyzer.parserInformation();
+        const parserInfo = analyzer.parserInformation();
         if (parserInfo.name === 'r-shell') {
             const object = (0, format_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(result.parsed));
             output.stdout(depthListToTextTree(toDepthMap(object), output.formatter));

package/cli/repl/commands/repl-query.js

@@ -29,15 +29,19 @@ async function processQueryArgs(output, analyzer, remainingArgs) {
         return;
     }
     let parsedQuery;
+    let input;
     if (query.startsWith('@')) {
         const queryName = query.slice(1);
         const queryObj = query_1.SupportedQueries[queryName];
         if (queryObj?.fromLine) {
-            const q = queryObj.fromLine(remainingArgs, analyzer.flowrConfig);
+            const parseResult = queryObj.fromLine(output, remainingArgs, analyzer.flowrConfig);
+            const q = parseResult.query;
             parsedQuery = q ? (Array.isArray(q) ? q : [q]) : [];
+            input = parseResult.rCode;
         }
         else {
             parsedQuery = [{ type: query.slice(1) }];
+            input = remainingArgs.join(' ').trim();
         }
         const validationResult = (0, query_1.QueriesSchema)().validate(parsedQuery);
         if (validationResult.error) {
@@ -54,10 +58,15 @@ async function processQueryArgs(output, analyzer, remainingArgs) {
             printHelp(output);
             return;
         }
+        input = remainingArgs.join(' ').trim();
     }
     else {
         parsedQuery = [{ type: 'call-context', callName: query }];
     }
+    if (input) {
+        analyzer.reset();
+        analyzer.addRequest((0, retriever_1.requestFromInput)(input));
+    }
     return {
         query: await (0, query_1.executeQueries)({
             analyzer,
@@ -68,13 +77,13 @@ async function processQueryArgs(output, analyzer, remainingArgs) {
 }
 /**
  * Function for splitting the input line.
- * The first token is the query command.
- * The rest of the line is treated as input code.
+ * All input is treated as arguments, no R code is separated so that the individual queries can handle it.
+ * @param line - The input line
  */
 function parseArgs(line) {
     const args = (0, args_1.splitAtEscapeSensitive)(line);
     return {
-        input: args[1].trim() === 'help' ? '' : args.slice(1).join(' ').trim(),
+        rCode: undefined,
         remaining: args
     };
 }
@@ -104,7 +113,9 @@ exports.queryStarCommand = {
     fn: async ({ output, analyzer, remainingArgs }) => {
         const results = await processQueryArgs(output, analyzer, remainingArgs);
         if (results) {
-            output.stdout(JSON.stringify(results.query, json_1.jsonReplacer));
+            const json = Object.fromEntries(Object.entries(results.query)
+                .map(([query, queryResults]) => [query, query_1.SupportedQueries[query]?.jsonFormatter?.(queryResults) ?? queryResults]));
+            output.stdout(JSON.stringify(json, json_1.jsonReplacer));
         }
     }
 };