@eagleoutice/flowr 2.1.11 → 2.2.0

package/benchmark/slicer.d.ts

@@ -12,6 +12,7 @@ import type { SlicingCriteria } from '../slicing/criterion/parse';
 import type { RParseRequestFromFile, RParseRequestFromText } from '../r-bridge/retriever';
 import type { SlicingCriteriaFilter } from '../slicing/criterion/collect-all';
 import type { AutoSelectPredicate } from '../reconstruct/auto-select/auto-select-defaults';
+import type { KnownParserName } from '../r-bridge/parser';
 /**
  * The logger to be used for benchmarking as a global object.
  */
@@ -42,29 +43,21 @@ export interface BenchmarkSingleSliceStats extends MergeableRecord {
     /** the final code, as the result of the 'reconstruct' step */
     code: ReconstructionResult;
 }
-/**
- * A slicer that can be used to slice exactly one file (multiple times).
- * It holds its own {@link RShell} instance, maintains a cached dataflow and keeps measurements.
- *
- * Make sure to call {@link init} to initialize the slicer, before calling {@link slice}.
- * After slicing, call {@link finish} to close the R session and retrieve the stats.
- *
- * @note Under the hood, the benchmark slicer maintains a {@link PipelineExecutor} using the {@link DEFAULT_SLICING_PIPELINE}.
- */
 export declare class BenchmarkSlicer {
     /** Measures all data recorded *once* per slicer (complete setup up to the dataflow graph creation) */
     private readonly commonMeasurements;
     private readonly perSliceMeasurements;
     private readonly deltas;
-    private readonly shell;
+    private readonly parserName;
     private stats;
     private loadedXml;
     private dataflow;
     private normalizedAst;
     private totalStopwatch;
     private finished;
-    private pipeline;
-    constructor();
+    private executor;
+    private parser;
+    constructor(parserName: KnownParserName);
     /**
      * Initialize the slicer on the given request.
      * Can only be called once for each instance.

package/benchmark/slicer.js

@@ -11,35 +11,27 @@ exports.BenchmarkSlicer = exports.benchmarkLogger = void 0;
 const stopwatch_1 = require("./stopwatch");
 const fs_1 = __importDefault(require("fs"));
 const log_1 = require("../util/log");
-const pipeline_executor_1 = require("../core/pipeline-executor");
 const assert_1 = require("../util/assert");
 const strings_1 = require("../util/strings");
-const shell_1 = require("../r-bridge/shell");
 const default_pipelines_1 = require("../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../r-bridge/retriever");
 const collect_all_1 = require("../slicing/criterion/collect-all");
 const type_1 = require("../r-bridge/lang-4.x/ast/model/type");
 const visitor_1 = require("../r-bridge/lang-4.x/ast/model/processing/visitor");
 const size_of_1 = require("./stats/size-of");
+const shell_1 = require("../r-bridge/shell");
+const tree_sitter_types_1 = require("../r-bridge/lang-4.x/tree-sitter/tree-sitter-types");
+const tree_sitter_executor_1 = require("../r-bridge/lang-4.x/tree-sitter/tree-sitter-executor");
 /**
  * The logger to be used for benchmarking as a global object.
  */
 exports.benchmarkLogger = log_1.log.getSubLogger({ name: 'benchmark' });
-/**
- * A slicer that can be used to slice exactly one file (multiple times).
- * It holds its own {@link RShell} instance, maintains a cached dataflow and keeps measurements.
- *
- * Make sure to call {@link init} to initialize the slicer, before calling {@link slice}.
- * After slicing, call {@link finish} to close the R session and retrieve the stats.
- *
- * @note Under the hood, the benchmark slicer maintains a {@link PipelineExecutor} using the {@link DEFAULT_SLICING_PIPELINE}.
- */
 class BenchmarkSlicer {
     /** Measures all data recorded *once* per slicer (complete setup up to the dataflow graph creation) */
     commonMeasurements = new stopwatch_1.Measurements();
     perSliceMeasurements = new Map();
     deltas = new Map();
-    shell;
+    parserName;
     stats;
     loadedXml;
     dataflow;
@@ -47,10 +39,11 @@ class BenchmarkSlicer {
     totalStopwatch;
     finished = false;
     // Yes, this is unclean, but we know that we assign the executor during the initialization and this saves us from having to check for nullability every time
-    pipeline = null;
-    constructor() {
+    executor = null;
+    parser = null;
+    constructor(parserName) {
         this.totalStopwatch = this.commonMeasurements.start('total');
-        this.shell = this.commonMeasurements.measure('initialize R session', () => new shell_1.RShell());
+        this.parserName = parserName;
     }
     /**
      * Initialize the slicer on the given request.
@@ -58,8 +51,17 @@ class BenchmarkSlicer {
      */
     async init(request, autoSelectIf) {
         (0, assert_1.guard)(this.stats === undefined, 'cannot initialize the slicer twice');
-        this.pipeline = new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_SLICING_PIPELINE, {
-            shell: this.shell,
+        // we know these are in sync so we just cast to one of them
+        this.parser = await this.commonMeasurements.measure('initialize R session', async () => {
+            if (this.parserName === 'r-shell') {
+                return new shell_1.RShell();
+            }
+            else {
+                await tree_sitter_executor_1.TreeSitterExecutor.initTreeSitter();
+                return new tree_sitter_executor_1.TreeSitterExecutor();
+            }
+        });
+        this.executor = (0, default_pipelines_1.createSlicePipeline)(this.parser, {
             request: { ...request },
             criterion: [],
             autoSelectIf
@@ -67,14 +69,30 @@ class BenchmarkSlicer {
         this.loadedXml = (await this.measureCommonStep('parse', 'retrieve AST from R code')).parsed;
         this.normalizedAst = await this.measureCommonStep('normalize', 'normalize R AST');
         this.dataflow = await this.measureCommonStep('dataflow', 'produce dataflow information');
-        this.pipeline.switchToRequestStage();
+        this.executor.switchToRequestStage();
         await this.calculateStatsAfterInit(request);
     }
     async calculateStatsAfterInit(request) {
         const loadedContent = request.request === 'text' ? request.content : fs_1.default.readFileSync(request.content, 'utf-8');
-        // retrieve number of R tokens - flowr_parsed should still contain the last parsed code
-        const numberOfRTokens = await (0, retriever_1.retrieveNumberOfRTokensOfLastParse)(this.shell);
-        const numberOfRTokensNoComments = await (0, retriever_1.retrieveNumberOfRTokensOfLastParse)(this.shell, true);
+        let numberOfRTokens;
+        let numberOfRTokensNoComments;
+        if (this.parser.name === 'r-shell') {
+            // retrieve number of R tokens - flowr_parsed should still contain the last parsed code
+            numberOfRTokens = await (0, retriever_1.retrieveNumberOfRTokensOfLastParse)(this.parser);
+            numberOfRTokensNoComments = await (0, retriever_1.retrieveNumberOfRTokensOfLastParse)(this.parser, true);
+        }
+        else {
+            const countChildren = function (node, ignoreComments = false) {
+                let ret = node.type === tree_sitter_types_1.TreeSitterType.Comment && ignoreComments ? 0 : 1;
+                for (const child of node.children) {
+                    ret += countChildren(child, ignoreComments);
+                }
+                return ret;
+            };
+            const root = this.loadedXml.rootNode;
+            numberOfRTokens = countChildren(root);
+            numberOfRTokensNoComments = countChildren(root, true);
+        }
         (0, assert_1.guard)(this.normalizedAst !== undefined, 'normalizedAst should be defined after initialization');
         (0, assert_1.guard)(this.dataflow !== undefined, 'dataflow should be defined after initialization');
         // collect dataflow graph size
@@ -165,14 +183,14 @@ class BenchmarkSlicer {
             }
         };
         this.perSliceMeasurements.set(slicingCriteria, stats);
-        this.pipeline.updateRequest({ criterion: slicingCriteria });
+        this.executor.updateRequest({ criterion: slicingCriteria });
         const totalStopwatch = measurements.start('total');
         const slicedOutput = await this.measureSliceStep('slice', measurements, 'static slicing');
         stats.slicingCriteria = [...slicedOutput.decodedCriteria];
         stats.reconstructedCode = await this.measureSliceStep('reconstruct', measurements, 'reconstruct code');
         totalStopwatch.stop();
         exports.benchmarkLogger.debug(`Produced code for ${JSON.stringify(slicingCriteria)}: ${stats.reconstructedCode.code}`);
-        const results = this.pipeline.getResults(false);
+        const results = this.executor.getResults(false);
         if (exports.benchmarkLogger.settings.minLevel >= 3 /* LogLevel.Info */) {
             exports.benchmarkLogger.info(`mapped slicing criteria: ${slicedOutput.decodedCriteria.map(c => {
                 const node = results.normalize.idMap.get(c.id);
@@ -192,7 +210,7 @@ class BenchmarkSlicer {
     /** Bridging the gap between the new internal and the old names for the benchmarking */
     async measureCommonStep(expectedStep, keyToMeasure) {
         const memoryInit = process.memoryUsage();
-        const { result } = await this.commonMeasurements.measureAsync(keyToMeasure, () => this.pipeline.nextStep(expectedStep));
+        const { result } = await this.commonMeasurements.measureAsync(keyToMeasure, () => this.executor.nextStep(expectedStep));
         const memoryEnd = process.memoryUsage();
         this.deltas.set(keyToMeasure, {
             heap: memoryEnd.heapUsed - memoryInit.heapUsed,
@@ -203,7 +221,7 @@ class BenchmarkSlicer {
         return result;
     }
     async measureSliceStep(expectedStep, measure, keyToMeasure) {
-        const { result } = await measure.measureAsync(keyToMeasure, () => this.pipeline.nextStep(expectedStep));
+        const { result } = await measure.measureAsync(keyToMeasure, () => this.executor.nextStep(expectedStep));
         return result;
     }
     guardActive() {
@@ -242,7 +260,7 @@ class BenchmarkSlicer {
     finish() {
         (0, assert_1.guard)(this.stats !== undefined, 'need to call init before finish');
         if (!this.finished) {
-            this.commonMeasurements.measure('close R session', () => this.shell.close());
+            this.commonMeasurements.measure('close R session', () => this.parser.close());
             this.totalStopwatch.stop();
             this.finished = true;
         }
@@ -268,7 +286,7 @@ class BenchmarkSlicer {
         };
         return {
             stats: this.stats,
-            parse: this.loadedXml,
+            parse: typeof this.loadedXml === 'string' ? this.loadedXml : JSON.stringify(this.loadedXml),
             dataflow: this.dataflow,
             normalize: this.normalizedAst
         };
@@ -277,7 +295,7 @@ class BenchmarkSlicer {
    * Only call in case of an error - if the session must be closed and the benchmark itself is to be considered failed/dead.
    */
     ensureSessionClosed() {
-        this.shell.close();
+        this.parser?.close();
     }
 }
 exports.BenchmarkSlicer = BenchmarkSlicer;

package/cli/benchmark-app.d.ts

@@ -1,3 +1,4 @@
+import type { KnownParserName } from '../r-bridge/parser';
 export interface BenchmarkCliOptions {
     verbose: boolean;
     help: boolean;
@@ -7,4 +8,5 @@ export interface BenchmarkCliOptions {
     parallel: number;
     limit?: number;
     runs?: number;
+    parser: KnownParserName;
 }

package/cli/benchmark-app.js

@@ -58,7 +58,8 @@ async function benchmark() {
         '--input', f.request.content,
         '--file-id', `${i}`,
         '--output', path_1.default.join(options.output, path_1.default.relative(f.baseDir, `${f.request.content}.json`)),
-        '--slice', options.slice, ...verboseAdd
+        '--slice', options.slice, ...verboseAdd,
+        '--parser', options.parser
     ]);
     const runs = options.runs ?? 1;
     for (let i = 1; i <= runs; i++) {

package/cli/benchmark-helper-app.d.ts

@@ -1,3 +1,4 @@
+import type { KnownParserName } from '../r-bridge/parser';
 export interface SingleBenchmarkCliOptions {
     verbose: boolean;
     help: boolean;
@@ -6,4 +7,5 @@ export interface SingleBenchmarkCliOptions {
     'run-num'?: number;
     slice: string;
     output?: string;
+    parser: KnownParserName;
 }

package/cli/benchmark-helper-app.js

@@ -36,7 +36,7 @@ async function benchmark() {
     const fileStat = fs_1.default.statSync(options.input);
     (0, assert_1.guard)(fileStat.isFile(), `File ${options.input} does not exist or is no file`);
     const request = { request: 'file', content: options.input };
-    const slicer = new slicer_1.BenchmarkSlicer();
+    const slicer = new slicer_1.BenchmarkSlicer(options.parser);
     try {
         await slicer.init(request);
         // ${escape}1F${escape}1G${escape}2K for line reset
@@ -69,7 +69,7 @@ async function benchmark() {
     catch (e) {
         if (e instanceof Error) {
             if (!e.message.includes('unable to parse R')) {
-                console.log(`${prefix} Non R-Side error : ${e.message}`);
+                console.log(`${prefix} Non R-Side error : ${e.name} ${e.message} ${e.stack}`);
             }
         }
         slicer.ensureSessionClosed(); // ensure finish

package/cli/common/options.js

@@ -19,7 +19,8 @@ exports.benchmarkOptions = [
     { name: 'input', alias: 'i', type: String, description: 'Pass a folder or file as src to read from', multiple: true, defaultOption: true, defaultValue: [], typeLabel: '{underline files/folders}' },
     { name: 'parallel', alias: 'p', type: String, description: 'Number of parallel executors (defaults to {italic max(cpu.count-1, 1)})', defaultValue: Math.max(os_1.default.cpus().length - 1, 1), typeLabel: '{underline number}' },
     { name: 'slice', alias: 's', type: String, description: 'Automatically slice for *all* variables (default) or *no* slicing and only parsing/dataflow construction. Numbers will indicate: sample X random slices from all.', defaultValue: 'all', typeLabel: '{underline all/no}' },
-    { name: 'output', alias: 'o', type: String, description: `Directory to write all the measurements to in a per-file-basis (defaults to {italic benchmark-${StartTimeString}})`, defaultValue: `benchmark-${StartTimeString}`, typeLabel: '{underline file}' }
+    { name: 'output', alias: 'o', type: String, description: `Directory to write all the measurements to in a per-file-basis (defaults to {italic benchmark-${StartTimeString}})`, defaultValue: `benchmark-${StartTimeString}`, typeLabel: '{underline file}' },
+    { name: 'parser', type: String, description: 'The parser to use for the benchmark', defaultValue: 'r-shell', typeLabel: '{underline parser}' }
 ];
 exports.benchmarkHelperOptions = [
     { name: 'verbose', alias: 'v', type: Boolean, description: 'Run with verbose logging [do not use for the real benchmark as this affects the time measurements, but only to find errors]' },
@@ -29,6 +30,7 @@ exports.benchmarkHelperOptions = [
     { name: 'run-num', alias: 'r', type: Number, description: 'The n-th time that the file with the given file-id is being benchmarked' },
     { name: 'slice', alias: 's', type: String, description: 'Automatically slice for *all* variables (default) or *no* slicing and only parsing/dataflow construction. Numbers will indicate: sample X random slices from all.', defaultValue: 'all', typeLabel: '{underline all/no}' },
     { name: 'output', alias: 'o', type: String, description: 'File to write the measurements to (appends a single line in JSON format)', typeLabel: '{underline file}' },
+    { name: 'parser', type: String, description: 'The parser to use for the benchmark', defaultValue: 'r-shell', typeLabel: '{underline parser}' }
 ];
 exports.exportQuadsOptions = [
     { name: 'verbose', alias: 'v', type: Boolean, description: 'Run with verbose logging' },

package/cli/flowr-main-options.js

@@ -47,7 +47,7 @@ exports.flowrMainOptionDefinitions = [
     {
         name: 'r-path',
         type: String,
-        description: 'The path to the R executable to use. Defaults to your PATH.',
+        description: 'The path to the R executable to use. Defaults to your PATH. This option is being phased out in favor of the engine configuration option "engine.r-shell.r-path", which should be used instead.',
         multiple: false
     },
     {
@@ -82,7 +82,41 @@ exports.flowrMainOptionDefinitions = [
         type: Boolean,
         description: 'Provide information about the version of flowR as well as its underlying R system and exit.'
     },
-    { name: 'ws', type: Boolean, description: 'If the server flag is set, use websocket for messaging' }
+    { name: 'ws', type: Boolean, description: 'If the server flag is set, use websocket for messaging' },
+    {
+        name: 'engine.r-shell.disabled',
+        type: Boolean,
+        description: 'Disable the R shell engine'
+    },
+    {
+        name: 'engine.r-shell.r-path',
+        type: String,
+        description: 'The path to the R executable to use. Defaults to your PATH.',
+        multiple: false
+    },
+    {
+        name: 'engine.tree-sitter.disabled',
+        type: Boolean,
+        description: 'Disable the tree-sitter engine'
+    },
+    {
+        name: 'engine.tree-sitter.wasm-path',
+        type: String,
+        description: 'The path to the tree-sitter-r WASM binary to use. Defaults to the one shipped with flowR.',
+        multiple: false
+    },
+    {
+        name: 'engine.tree-sitter.tree-sitter-wasm-path',
+        type: String,
+        description: 'The path to the tree-sitter WASM binary to use. Defaults to the path specified by the tree-sitter package.',
+        multiple: false
+    },
+    {
+        name: 'default-engine',
+        type: String,
+        description: 'The default engine to use for interacting with R code. If this is undefined, an arbitrary engine from the specified list will be used.',
+        multiple: false
+    }
 ];
 exports.defaultConfigFile = 'flowr.json';
 //# sourceMappingURL=flowr-main-options.js.map

package/cli/flowr.d.ts

@@ -14,6 +14,12 @@ export interface FlowrCliOptions {
     verbose: boolean;
     version: boolean;
     ws: boolean;
+    'default-engine': string;
+    'engine.r-shell.disabled': boolean;
+    'engine.r-shell.r-path': string | undefined;
+    'engine.tree-sitter.disabled': boolean;
+    'engine.tree-sitter.wasm-path': string | undefined;
+    'engine.tree-sitter.tree-sitter-wasm-path': string | undefined;
 }
 export declare const optionHelp: ({
     header: string;

package/cli/flowr.js

@@ -21,6 +21,7 @@ const core_1 = require("./repl/core");
 const repl_version_1 = require("./repl/commands/repl-version");
 const print_version_1 = require("./repl/print-version");
 const flowr_main_options_1 = require("./flowr-main-options");
+const tree_sitter_executor_1 = require("../r-bridge/lang-4.x/tree-sitter/tree-sitter-executor");
 const fs_1 = __importDefault(require("fs"));
 exports.toolName = 'flowr';
 exports.optionHelp = [
@@ -69,20 +70,44 @@ if (!usedConfig) {
     }
     (0, config_1.setConfigFile)(options['config-file'] ?? flowr_main_options_1.defaultConfigFile, undefined, true);
 }
-function retrieveShell() {
-    // we keep an active shell session to allow other parse investigations :)
-    let opts = {
-        revive: 2 /* RShellReviveOptions.Always */,
-        onRevive: (code, signal) => {
-            const signalText = signal == null ? '' : ` and signal ${signal}`;
-            console.log(ansi_1.formatter.format(`R process exited with code ${code}${signalText}. Restarting...`, { color: 5 /* Colors.Magenta */, effect: ansi_1.ColorEffect.Foreground }));
-            console.log((0, ansi_1.italic)(`If you want to exit, press either Ctrl+C twice, or enter ${(0, ansi_1.bold)(':quit')}`));
-        }
-    };
-    if (options['r-path']) {
-        opts = { ...opts, pathToRExecutable: options['r-path'] };
+// for all options that we manually supply that have a config equivalent, set them in the config
+if (!options['engine.r-shell.disabled']) {
+    (0, config_1.amendConfig)({ engines: [{ type: 'r-shell', rPath: options['r-path'] || options['engine.r-shell.r-path'] }] });
+}
+if (!options['engine.tree-sitter.disabled']) {
+    (0, config_1.amendConfig)({ engines: [{
+                type: 'tree-sitter',
+                wasmPath: options['engine.tree-sitter.wasm-path'],
+                treeSitterWasmPath: options['engine.tree-sitter.tree-sitter-wasm-path']
+            }] });
+}
+if (options['default-engine']) {
+    (0, config_1.amendConfig)({ defaultEngine: options['default-engine'] });
+}
+async function retrieveEngineInstances() {
+    const engines = {};
+    if ((0, config_1.getEngineConfig)('r-shell')) {
+        // we keep an active shell session to allow other parse investigations :)
+        engines['r-shell'] = new shell_1.RShell({
+            revive: 2 /* RShellReviveOptions.Always */,
+            onRevive: (code, signal) => {
+                const signalText = signal == null ? '' : ` and signal ${signal}`;
+                console.log(ansi_1.formatter.format(`R process exited with code ${code}${signalText}. Restarting...`, { color: 5 /* Colors.Magenta */, effect: ansi_1.ColorEffect.Foreground }));
+                console.log((0, ansi_1.italic)(`If you want to exit, press either Ctrl+C twice, or enter ${(0, ansi_1.bold)(':quit')}`));
+            }
+        });
+    }
+    if ((0, config_1.getEngineConfig)('tree-sitter')) {
+        await tree_sitter_executor_1.TreeSitterExecutor.initTreeSitter();
+        engines['tree-sitter'] = new tree_sitter_executor_1.TreeSitterExecutor();
     }
-    return new shell_1.RShell(opts);
+    let defaultEngine = (0, config_1.getConfig)().defaultEngine;
+    if (!defaultEngine || !engines[defaultEngine]) {
+        // if a default engine isn't specified, we just take the first one we have
+        defaultEngine = Object.keys(engines)[0];
+    }
+    log_1.log.info(`Using engines ${Object.keys(engines).join(', ')} with default ${defaultEngine}`);
+    return { engines, default: defaultEngine };
 }
 async function mainRepl() {
     if (options.script) {
@@ -97,18 +122,20 @@ async function mainRepl() {
         console.log((0, command_line_usage_1.default)(exports.optionHelp));
         process.exit(0);
     }
+    const engines = await retrieveEngineInstances();
+    const defaultEngine = engines.engines[engines.default];
     if (options.version) {
-        const shell = new shell_1.RShell();
-        process.on('exit', () => shell.close());
-        await (0, repl_version_1.printVersionInformation)(repl_main_1.standardReplOutput, shell);
+        for (const engine of Object.values(engines.engines)) {
+            await (0, repl_version_1.printVersionInformation)(repl_main_1.standardReplOutput, engine);
+            engine?.close();
+        }
         process.exit(0);
     }
-    const shell = retrieveShell();
     const end = () => {
         if (options.execute === undefined) {
             console.log(`\n${(0, ansi_1.italic)('Exiting...')}`);
         }
-        shell.close();
+        Object.values(engines.engines).forEach(e => e?.close());
         process.exit(0);
     };
     // hook some handlers
@@ -116,27 +143,27 @@ async function mainRepl() {
     process.on('SIGTERM', end);
     const allowRSessionAccess = options['r-session-access'] ?? false;
     if (options.execute) {
-        await (0, core_1.replProcessAnswer)(repl_main_1.standardReplOutput, options.execute, shell, allowRSessionAccess);
+        await (0, core_1.replProcessAnswer)(repl_main_1.standardReplOutput, options.execute, defaultEngine, allowRSessionAccess);
     }
     else {
-        await (0, print_version_1.printVersionRepl)(shell);
-        await (0, core_1.repl)({ shell, allowRSessionAccess });
+        await (0, print_version_1.printVersionRepl)(defaultEngine);
+        await (0, core_1.repl)({ parser: defaultEngine, allowRSessionAccess });
     }
     process.exit(0);
 }
 async function mainServer(backend = new net_1.NetServer()) {
-    const shell = retrieveShell();
+    const engines = await retrieveEngineInstances();
     const end = () => {
         if (options.execute === undefined) {
             console.log(`\n${(0, ansi_1.italic)('Exiting...')}`);
         }
-        shell.close();
+        Object.values(engines.engines).forEach(e => e?.close());
         process.exit(0);
     };
     // hook some handlers
     process.on('SIGINT', end);
     process.on('SIGTERM', end);
-    await new server_1.FlowRServer(shell, options['r-session-access'], backend).start(options.port);
+    await new server_1.FlowRServer(engines.engines, engines.default, options['r-session-access'], backend).start(options.port);
 }
 if (options.server) {
     void mainServer(options.ws ? new net_1.WebSocketServerWrapper() : new net_1.NetServer());

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

@@ -1,14 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.controlflowStarCommand = exports.controlflowCommand = void 0;
-const pipeline_executor_1 = require("../../../core/pipeline-executor");
 const cfg_1 = require("../../../util/cfg/cfg");
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../../r-bridge/retriever");
 const cfg_2 = require("../../../util/mermaid/cfg");
-async function controlflow(shell, remainingLine) {
-    return await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_NORMALIZE_PIPELINE, {
-        shell,
+async function controlflow(parser, remainingLine) {
+    return await (0, default_pipelines_1.createNormalizePipeline)(parser, {
         request: (0, retriever_1.requestFromInput)(remainingLine.trim())
     }).allRemainingSteps();
 }

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

@@ -1,13 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.dataflowStarCommand = exports.dataflowCommand = void 0;
-const pipeline_executor_1 = require("../../../core/pipeline-executor");
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../../r-bridge/retriever");
 const dfg_1 = require("../../../util/mermaid/dfg");
-async function dataflow(shell, remainingLine) {
-    return await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
-        shell,
+async function dataflow(parser, remainingLine) {
+    return await (0, default_pipelines_1.createDataflowPipeline)(parser, {
         request: (0, retriever_1.requestFromInput)(remainingLine.trim())
     }).allRemainingSteps();
 }

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

@@ -1,4 +1,4 @@
 import type { ReplCommand, ReplOutput } from './repl-main';
-import type { RShell } from '../../../r-bridge/shell';
-export declare function executeRShellCommand(output: ReplOutput, shell: RShell, statement: string): Promise<void>;
+import type { KnownParser } from '../../../r-bridge/parser';
+export declare function tryExecuteRShellCommand(output: ReplOutput, parser: KnownParser, statement: string, allowRSessionAccess: boolean): Promise<void>;
 export declare const executeCommand: ReplCommand;

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

@@ -1,8 +1,20 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.executeCommand = void 0;
-exports.executeRShellCommand = executeRShellCommand;
+exports.tryExecuteRShellCommand = tryExecuteRShellCommand;
 const ansi_1 = require("../../../util/ansi");
+const shell_1 = require("../../../r-bridge/shell");
+async function tryExecuteRShellCommand(output, parser, statement, allowRSessionAccess) {
+    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 })}\nIf you want to do so, please restart flowR with the ${output.formatter.format('--r-session-access', { style: 1 /* FontStyles.Bold */ })} flag. Please be careful of the security implications of this action.`);
+    }
+    else if (parser instanceof shell_1.RShell) {
+        await executeRShellCommand(output, parser, statement);
+    }
+    else {
+        output.stderr(`Executing arbitrary R code is only possible when using the r-shell engine as the default engine. Enable it using the configuration file or the ${output.formatter.format('--default-engine r-shell', { style: 1 /* FontStyles.Bold */ })} command line option.`);
+    }
+}
 async function executeRShellCommand(output, shell, statement) {
     try {
         const result = await shell.sendCommandWithOutput(statement, {
@@ -16,12 +28,10 @@ async function executeRShellCommand(output, shell, statement) {
     }
 }
 exports.executeCommand = {
-    description: 'Execute the given code as R code (essentially similar to using now command)',
+    description: 'Execute the given code as R code (essentially similar to using now command). This requires the `--r-session-access` flag to be set and requires the r-shell engine.',
     usageExample: ':execute',
     aliases: ['e', 'r'],
     script: false,
-    fn: async (output, shell, remainingLine) => {
-        await executeRShellCommand(output, shell, remainingLine);
-    }
+    fn: tryExecuteRShellCommand
 };
 //# sourceMappingURL=repl-execute.js.map

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

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.lineageCommand = void 0;
 exports.getLineage = getLineage;
-const pipeline_executor_1 = require("../../../core/pipeline-executor");
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../../r-bridge/retriever");
 const parse_1 = require("../../../slicing/criterion/parse");
@@ -11,9 +10,8 @@ const assert_1 = require("../../../util/assert");
 function splitAt(str, idx) {
     return [str.slice(0, idx), str.slice(idx)];
 }
-async function getDfg(shell, remainingLine) {
-    return await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
-        shell,
+async function getDfg(parser, remainingLine) {
+    return await (0, default_pipelines_1.createDataflowPipeline)(parser, {
         request: (0, retriever_1.requestFromInput)(remainingLine.trim())
     }).allRemainingSteps();
 }

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

@@ -1,5 +1,5 @@
 import type { OutputFormatter } from '../../../util/ansi';
-import type { RShell } from '../../../r-bridge/shell';
+import type { KnownParser } from '../../../r-bridge/parser';
 /**
  * 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).
@@ -35,5 +35,5 @@ export interface ReplCommand {
      * Function to execute when the command is invoked, it must not write to the command line but instead use the output handler.
      * Furthermore, it has to obey the formatter defined in the {@link ReplOutput}.
      */
-    fn: (output: ReplOutput, shell: RShell, remainingLine: string) => Promise<void> | void;
+    fn: (output: ReplOutput, parser: KnownParser, remainingLine: string, allowRSessionAccess: boolean) => Promise<void> | void;
 }

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

@@ -1,13 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.normalizeStarCommand = exports.normalizeCommand = void 0;
-const pipeline_executor_1 = require("../../../core/pipeline-executor");
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../../r-bridge/retriever");
 const ast_1 = require("../../../util/mermaid/ast");
-async function normalize(shell, remainingLine) {
-    return await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_NORMALIZE_PIPELINE, {
-        shell,
+async function normalize(parser, remainingLine) {
+    return await (0, default_pipelines_1.createNormalizePipeline)(parser, {
         request: (0, retriever_1.requestFromInput)(remainingLine.trim())
     }).allRemainingSteps();
 }

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

@@ -1,7 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseCommand = void 0;
-const pipeline_executor_1 = require("../../../core/pipeline-executor");
 const format_1 = require("../../../r-bridge/lang-4.x/ast/parser/json/format");
 const normalize_meta_1 = require("../../../r-bridge/lang-4.x/ast/parser/main/normalize-meta");
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
@@ -90,9 +89,8 @@ exports.parseCommand = {
     usageExample: ':parse',
     aliases: ['p'],
     script: false,
-    fn: async (output, shell, remainingLine) => {
-        const result = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_PARSE_PIPELINE, {
-            shell,
+    fn: async (output, parser, remainingLine) => {
+        const result = await (0, default_pipelines_1.createParsePipeline)(parser, {
             request: (0, retriever_1.requestFromInput)((0, retriever_1.removeRQuotes)(remainingLine.trim()))
         }).allRemainingSteps();
         const object = (0, format_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(result.parse.parsed));