@eagleoutice/flowr 1.4.1 → 1.4.2

package/cli/repl/commands/quit.js

@@ -7,6 +7,9 @@ exports.quitCommand = {
     aliases: ['q', 'exit'],
     usageExample: ':quit',
     script: false,
-    fn: () => { log_1.log.info('bye'); process.exit(0); }
+    fn: () => {
+        log_1.log.info('bye');
+        process.exit(0);
+    }
 };
 //# sourceMappingURL=quit.js.map

package/cli/repl/core.d.ts

@@ -6,7 +6,7 @@
  */
 import { RShell } from '../../r-bridge';
 import type { ReplOutput } from './commands';
-import * as readline from 'node:readline';
+import * as readline from 'readline';
 /**
  * Used by the repl to provide automatic completions for a given (partial) input line
  */
@@ -32,8 +32,10 @@ export declare function replProcessAnswer(output: ReplOutput, expr: string, shel
  *                    If you want to provide a custom one but use the same `completer`, refer to {@link replCompleter}.
  *                    For the default arguments, see {@link DEFAULT_REPL_READLINE_CONFIGURATION}.
  * @param output    - Defines two methods that every function in the repl uses to output its data.
+ * @param historyFile - The file to use for persisting the repl's history. Passing undefined causes history not to be saved.
  *
  * For the execution, this function makes use of {@link replProcessAnswer}
  *
  */
-export declare function repl(shell?: RShell, rl?: readline.Interface, output?: ReplOutput): Promise<void>;
+export declare function repl(shell?: RShell, rl?: readline.Interface, output?: ReplOutput, historyFile?: string | undefined): Promise<void>;
+export declare function loadReplHistory(historyFile: string): string[] | undefined;

package/cli/repl/core.js

@@ -22,8 +22,11 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.repl = exports.replProcessAnswer = exports.DEFAULT_REPL_READLINE_CONFIGURATION = exports.replCompleter = void 0;
+exports.loadReplHistory = exports.repl = exports.replProcessAnswer = exports.DEFAULT_REPL_READLINE_CONFIGURATION = exports.replCompleter = void 0;
 /**
  * Basically a helper file to allow the main 'flowr' script (located in the source root) to provide its repl
  *
@@ -33,15 +36,51 @@ const r_bridge_1 = require("../../r-bridge");
 const statistics_1 = require("../../statistics");
 const prompt_1 = require("./prompt");
 const commands_1 = require("./commands");
-const readline = __importStar(require("node:readline"));
+const readline = __importStar(require("readline"));
 const args_1 = require("../../util/args");
 const execute_1 = require("./commands/execute");
-const replCompleterKeywords = Array.from(commands_1.commandNames, s => `:${s}`);
+const os_1 = __importDefault(require("os"));
+const path_1 = __importDefault(require("path"));
+const fs_1 = __importDefault(require("fs"));
+const common_1 = require("../common");
+let _replCompleterKeywords = undefined;
+function replCompleterKeywords() {
+    if (_replCompleterKeywords === undefined) {
+        _replCompleterKeywords = Array.from((0, commands_1.getCommandNames)(), s => `:${s}`);
+    }
+    return _replCompleterKeywords;
+}
+const defaultHistoryFile = path_1.default.join(os_1.default.tmpdir(), '.flowrhistory');
 /**
  * Used by the repl to provide automatic completions for a given (partial) input line
  */
 function replCompleter(line) {
-    return [replCompleterKeywords.filter(k => k.startsWith(line)), line];
+    const splitLine = (0, args_1.splitAtEscapeSensitive)(line);
+    // did we just type a space (and are starting a new arg right now)?
+    const startingNewArg = line.endsWith(' ');
+    // if we typed a command fully already, autocomplete the arguments
+    if (splitLine.length > 1 || startingNewArg) {
+        const commandNameColon = replCompleterKeywords().find(k => splitLine[0] === k);
+        if (commandNameColon) {
+            const completions = [];
+            const commandName = commandNameColon.slice(1);
+            if ((0, commands_1.getCommand)(commandName)?.script === true) {
+                // autocomplete script arguments
+                const options = common_1.scripts[commandName].options;
+                completions.push(...(0, common_1.getValidOptionsForCompletion)(options, splitLine).map(o => `${o} `));
+            }
+            else {
+                // autocomplete command arguments (specifically, autocomplete the file:// protocol)
+                completions.push(r_bridge_1.fileProtocol);
+            }
+            // add an empty option so that it doesn't autocomplete the only defined option immediately
+            completions.push(' ');
+            const currentArg = startingNewArg ? '' : splitLine[splitLine.length - 1];
+            return [completions.filter(a => a.startsWith(currentArg)), currentArg];
+        }
+    }
+    // if no command is already typed, just return all commands that match
+    return [replCompleterKeywords().filter(k => k.startsWith(line)).map(k => `${k} `), line];
 }
 exports.replCompleter = replCompleter;
 exports.DEFAULT_REPL_READLINE_CONFIGURATION = {
@@ -49,6 +88,7 @@ exports.DEFAULT_REPL_READLINE_CONFIGURATION = {
     output: process.stdout,
     tabSize: 4,
     terminal: true,
+    history: loadReplHistory(defaultHistoryFile),
     removeHistoryDuplicates: true,
     completer: replCompleter
 };
@@ -57,7 +97,12 @@ async function replProcessStatement(output, statement, shell) {
         const command = statement.slice(1).split(' ')[0].toLowerCase();
         const processor = (0, commands_1.getCommand)(command);
         if (processor) {
-            await processor.fn(output, shell, statement.slice(command.length + 2).trim());
+            try {
+                await processor.fn(output, shell, statement.slice(command.length + 2).trim());
+            }
+            catch (e) {
+                console.log(`${(0, statistics_1.bold)(`Failed to execute command ${command}`)}: ${e?.message}. Using the ${(0, statistics_1.bold)('--verbose')} flag on startup may provide additional information.`);
+            }
         }
         else {
             console.log(`the command '${command}' is unknown, try ${(0, statistics_1.bold)(':help')} for more information`);
@@ -75,7 +120,7 @@ async function replProcessStatement(output, statement, shell) {
  * @param shell    - The {@link RShell} to use (see {@link repl}).
  */
 async function replProcessAnswer(output, expr, shell) {
-    const statements = (0, args_1.splitAtEscapeSensitive)(expr, ';');
+    const statements = (0, args_1.splitAtEscapeSensitive)(expr, false, ';');
     for (const statement of statements) {
         await replProcessStatement(output, statement, shell);
     }
@@ -93,11 +138,15 @@ exports.replProcessAnswer = replProcessAnswer;
  *                    If you want to provide a custom one but use the same `completer`, refer to {@link replCompleter}.
  *                    For the default arguments, see {@link DEFAULT_REPL_READLINE_CONFIGURATION}.
  * @param output    - Defines two methods that every function in the repl uses to output its data.
+ * @param historyFile - The file to use for persisting the repl's history. Passing undefined causes history not to be saved.
  *
  * For the execution, this function makes use of {@link replProcessAnswer}
  *
  */
-async function repl(shell = new r_bridge_1.RShell({ revive: 'always' }), rl = readline.createInterface(exports.DEFAULT_REPL_READLINE_CONFIGURATION), output = commands_1.standardReplOutput) {
+async function repl(shell = new r_bridge_1.RShell({ revive: 'always' }), rl = readline.createInterface(exports.DEFAULT_REPL_READLINE_CONFIGURATION), output = commands_1.standardReplOutput, historyFile = defaultHistoryFile) {
+    if (historyFile) {
+        rl.on('history', h => fs_1.default.writeFileSync(historyFile, h.join('\n'), { encoding: 'utf-8' }));
+    }
     // the incredible repl :D, we kill it with ':quit'
     // eslint-disable-next-line no-constant-condition,@typescript-eslint/no-unnecessary-condition
     while (true) {
@@ -113,4 +162,11 @@ async function repl(shell = new r_bridge_1.RShell({ revive: 'always' }), rl = re
     }
 }
 exports.repl = repl;
+function loadReplHistory(historyFile) {
+    if (!fs_1.default.existsSync(historyFile)) {
+        return undefined;
+    }
+    return fs_1.default.readFileSync(historyFile, { encoding: 'utf-8' }).split('\n');
+}
+exports.loadReplHistory = loadReplHistory;
 //# sourceMappingURL=core.js.map

package/cli/repl/execute.d.ts

@@ -1,5 +1,5 @@
 /// <reference types="node" />
-import type { Readable, Writable } from 'node:stream';
+import type { Readable, Writable } from 'stream';
 type Stdio = [stdin: Writable | null, stdout: Readable | null, stderr: Readable | null, extra: Writable | Readable | null | undefined, extra: Writable | Readable | null | undefined];
 export type StdioProcessor = (stdio: Stdio) => void;
 /**

package/cli/repl/execute.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.waitOnScript = exports.stdioCaptureProcessor = void 0;
 const log_1 = require("../../util/log");
 const child_process_1 = __importDefault(require("child_process"));
-const node_readline_1 = __importDefault(require("node:readline"));
+const readline_1 = __importDefault(require("readline"));
 const assert_1 = require("../../util/assert");
 /**
  * Simply captures the output of the script executed by {@link waitOnScript}.
@@ -17,12 +17,12 @@ const assert_1 = require("../../util/assert");
  */
 function stdioCaptureProcessor(stdio, onStdOutLine, onStdErrLine) {
     (0, assert_1.guard)(stdio[1] !== null, 'no stdout given in stdio!');
-    const outRl = node_readline_1.default.createInterface({
+    const outRl = readline_1.default.createInterface({
         input: stdio[1],
         terminal: false
     });
     (0, assert_1.guard)(stdio[2] !== null, 'no stderr given in stdio!');
-    const errRl = node_readline_1.default.createInterface({
+    const errRl = readline_1.default.createInterface({
         input: stdio[2],
         terminal: false
     });

package/cli/repl/server/connection.js

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FlowRServerConnection = void 0;
 const core_1 = require("../../../core");
-const r_bridge_1 = require("../../../r-bridge");
 const send_1 = require("./send");
 const validate_1 = require("./validate");
 const analysis_1 = require("./messages/analysis");
@@ -11,7 +10,6 @@ const server_1 = require("./server");
 const repl_1 = require("./messages/repl");
 const core_2 = require("../core");
 const statistics_1 = require("../../../statistics");
-const objects_1 = require("../../../util/objects");
 const cfg_1 = require("../../../util/cfg/cfg");
 const quads_1 = require("../../../util/quads");
 /**
@@ -100,7 +98,6 @@ class FlowRServerConnection {
             cfg = (0, cfg_1.extractCFG)(results.normalize);
         }
         const config = () => ({ context: message.filename ?? 'unknown', getId: (0, quads_1.defaultQuadIdGenerator)() });
-        const parseConfig = (0, objects_1.deepMergeObject)(r_bridge_1.DEFAULT_XML_PARSER_CONFIG, { tokenMap: await this.shell.tokenMap() });
         if (message.format === 'n-quads') {
             (0, send_1.sendMessage)(this.socket, {
                 type: 'response-file-analysis',
@@ -108,10 +105,9 @@ class FlowRServerConnection {
                 id: message.id,
                 cfg: cfg ? (0, cfg_1.cfg2quads)(cfg, config()) : undefined,
                 results: {
-                    parse: await (0, core_1.printStepResult)('parse', results.parse, 5 /* StepOutputFormat.RdfQuads */, config(), parseConfig),
+                    parse: await (0, core_1.printStepResult)('parse', results.parse, 5 /* StepOutputFormat.RdfQuads */, config()),
                     normalize: await (0, core_1.printStepResult)('normalize', results.normalize, 5 /* StepOutputFormat.RdfQuads */, config()),
-                    dataflow: await (0, core_1.printStepResult)('dataflow', results.dataflow, 5 /* StepOutputFormat.RdfQuads */, config()),
-                    ai: ''
+                    dataflow: await (0, core_1.printStepResult)('dataflow', results.dataflow, 5 /* StepOutputFormat.RdfQuads */, config())
                 }
             });
         }
@@ -138,8 +134,7 @@ class FlowRServerConnection {
             // we have to make sure, that the content is not interpreted as a file path if it starts with 'file://' therefore, we do it manually
             request: {
                 request: message.content === undefined ? 'file' : 'text',
-                content: message.content ?? message.filepath,
-                ensurePackageInstalled: false
+                content: message.content ?? message.filepath
             },
             criterion: [] // currently unknown
         });

package/cli/repl/server/net.js

@@ -7,7 +7,7 @@ exports.NetServer = exports.WebSocketWrapper = exports.WebSocketServerWrapper =
 /**
  * This is just a simple layer to allow me to mock the server's behavior in tests.
  */
-const node_net_1 = __importDefault(require("node:net"));
+const net_1 = __importDefault(require("net"));
 const ws_1 = require("ws");
 const server_1 = require("./server");
 class WebSocketServerWrapper {
@@ -50,7 +50,7 @@ exports.WebSocketWrapper = WebSocketWrapper;
 class NetServer {
     server;
     constructor() {
-        this.server = node_net_1.default.createServer();
+        this.server = net_1.default.createServer();
     }
     onConnect(handler) {
         this.server.on('connection', handler);

package/cli/statistics-helper-app.js

@@ -37,7 +37,6 @@ if (options.compress) {
 // assume correct
 const processedFeatures = new Set(options.features);
 const shell = new r_bridge_1.RShell();
-shell.tryToInjectHomeLibPath();
 (0, statistics_1.initFileProvider)(options['output-dir']);
 function compressFolder(folder, target) {
     // eslint-disable-next-line @typescript-eslint/no-unsafe-call,@typescript-eslint/no-unsafe-member-access

package/cli/summarizer-app.js

@@ -25,9 +25,8 @@ function getBenchmarkSummarizer() {
     return new summarizer_1.BenchmarkSummarizer({
         graphOutputPath: options.graph ? `${outputBase}-graph.json` : undefined,
         inputPath: options.input,
-        intermediateOutputPath: `${outputBase}.json`,
+        intermediateOutputPath: outputBase,
         outputPath: `${outputBase}-ultimate.json`,
-        outputLogPath: `${outputBase}.log`,
         logger: console.log
     });
 }

package/config.d.ts

@@ -0,0 +1,16 @@
+import type { MergeableRecord } from './util/objects';
+export interface FlowrConfigOptions extends MergeableRecord {
+    /**
+     * Whether source calls should be ignored, causing {@link processSourceCall}'s behavior to be skipped
+     */
+    ignoreSourceCalls: boolean;
+    /**
+     * The path to the R executable to use. If this is undefined, {@link DEFAULT_R_PATH} will be used.
+     */
+    rPath: string | undefined;
+}
+export declare const defaultConfigOptions: FlowrConfigOptions;
+export declare const defaultConfigFile = "flowr.json";
+export declare function setConfigFile(workingDirectory?: string, file?: string, forceLoad?: boolean): void;
+export declare function setConfig(config: FlowrConfigOptions): void;
+export declare function getConfig(): FlowrConfigOptions;

package/config.js

@@ -0,0 +1,75 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getConfig = exports.setConfig = exports.setConfigFile = exports.defaultConfigFile = exports.defaultConfigOptions = void 0;
+const objects_1 = require("./util/objects");
+const path_1 = __importDefault(require("path"));
+const fs_1 = __importDefault(require("fs"));
+const log_1 = require("./util/log");
+const files_1 = require("./util/files");
+const joi_1 = __importDefault(require("joi"));
+exports.defaultConfigOptions = {
+    ignoreSourceCalls: false,
+    rPath: undefined
+};
+exports.defaultConfigFile = 'flowr.json';
+const schema = joi_1.default.object({
+    ignoreSourceCalls: joi_1.default.boolean().optional()
+});
+let configWorkingDirectory = process.cwd();
+let configFile = exports.defaultConfigFile;
+let currentConfig;
+function setConfigFile(workingDirectory = process.cwd(), file = exports.defaultConfigFile, forceLoad = false) {
+    configWorkingDirectory = workingDirectory;
+    configFile = file;
+    // reset the config so it gets reloaded
+    currentConfig = undefined;
+    if (forceLoad) {
+        getConfig();
+    }
+}
+exports.setConfigFile = setConfigFile;
+function setConfig(config) {
+    currentConfig = config;
+}
+exports.setConfig = setConfig;
+function getConfig() {
+    // lazy-load the config based on the current settings
+    if (currentConfig === undefined) {
+        setConfig(parseConfigOptions(configWorkingDirectory, configFile));
+    }
+    return currentConfig;
+}
+exports.getConfig = getConfig;
+function parseConfigOptions(workingDirectory, configFile) {
+    let searchPath = path_1.default.resolve(workingDirectory);
+    do {
+        const configPath = path_1.default.join(searchPath, configFile);
+        if (fs_1.default.existsSync(configPath)) {
+            try {
+                const text = fs_1.default.readFileSync(configPath, { encoding: 'utf-8' });
+                const parsed = JSON.parse(text);
+                const validate = schema.validate(parsed);
+                if (!validate.error) {
+                    // assign default values to all config options except for the specified ones
+                    const ret = (0, objects_1.deepMergeObject)(exports.defaultConfigOptions, parsed);
+                    log_1.log.info(`Using config ${JSON.stringify(ret)} from ${configPath}`);
+                    return ret;
+                }
+                else {
+                    log_1.log.error(`Failed to validate config file at ${configPath}: ${validate.error.message}`);
+                }
+            }
+            catch (e) {
+                log_1.log.error(`Failed to parse config file at ${configPath}: ${e.message}`);
+            }
+        }
+        // move up to parent directory
+        searchPath = (0, files_1.getParentDirectory)(searchPath);
+    } while (fs_1.default.existsSync(searchPath));
+    log_1.log.info(`Using default config ${JSON.stringify(exports.defaultConfigOptions)}`);
+    return exports.defaultConfigOptions;
+}
+//# sourceMappingURL=config.js.map

package/core/input.d.ts

@@ -27,7 +27,7 @@ interface BaseSteppingSlicerInput<InterestedIn extends StepName | undefined> ext
     /** If you want to auto-select something in the reconstruction add it here, otherwise, it will use the default defined alongside {@link reconstructToCode}*/
     autoSelectIf?: AutoSelectPredicate;
 }
-interface NormalizeSteppingSlicerInput<InterestedIn extends 'ai' | 'dataflow' | 'normalize'> extends BaseSteppingSlicerInput<InterestedIn> {
+interface NormalizeSteppingSlicerInput<InterestedIn extends 'dataflow' | 'normalize'> extends BaseSteppingSlicerInput<InterestedIn> {
     stepOfInterest: InterestedIn;
 }
 interface SliceSteppingSlicerInput<InterestedIn extends 'reconstruct' | 'slice' | undefined> extends BaseSteppingSlicerInput<InterestedIn> {

package/core/output.d.ts

@@ -9,8 +9,7 @@ type StepResultsHelper<InterestedIn extends StepName> = {
     'parse': Out<'parse'>;
     'normalize': StepResultsHelper<'parse'> & Out<'normalize'>;
     'dataflow': StepResultsHelper<'normalize'> & Out<'dataflow'>;
-    'ai': StepResultsHelper<'dataflow'> & Out<'ai'>;
-    'slice': StepResultsHelper<'ai'> & Out<'slice'>;
+    'slice': StepResultsHelper<'dataflow'> & Out<'slice'>;
     'reconstruct': StepResultsHelper<'slice'> & Out<'reconstruct'>;
 }[InterestedIn];
 export {};

package/core/print/parse-printer.d.ts

@@ -1,3 +1,2 @@
 import type { QuadSerializationConfiguration } from '../../util/quads';
-import type { XmlParserConfig } from '../../r-bridge';
-export declare function parseToQuads(code: string, config: QuadSerializationConfiguration, parseConfig: XmlParserConfig): Promise<string>;
+export declare function parseToQuads(code: string, config: QuadSerializationConfiguration): string;

package/core/print/parse-printer.js

@@ -2,7 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseToQuads = void 0;
 const quads_1 = require("../../util/quads");
-const internal_1 = require("../../r-bridge/lang-4.x/ast/parser/xml/internal");
+const r_bridge_1 = require("../../r-bridge");
+const format_1 = require("../../r-bridge/lang-4.x/ast/parser/json/format");
+const parser_1 = require("../../r-bridge/lang-4.x/ast/parser/json/parser");
 function filterObject(obj, keys) {
     if (typeof obj !== 'object') {
         return obj;
@@ -20,10 +22,10 @@ function filterObject(obj, keys) {
             .map(([k, v]) => [k, filterObject(v, keys)]));
     }
 }
-async function parseToQuads(code, config, parseConfig) {
-    const obj = await (0, internal_1.xlm2jsonObject)(parseConfig, code);
+function parseToQuads(code, config) {
+    const obj = (0, parser_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(code));
     // recursively filter so that if the object contains one of the keys 'a', 'b' or 'c', all other keys are ignored
-    return (0, quads_1.serialize2quads)(filterObject(obj, new Set([parseConfig.attributeName, parseConfig.childrenName, parseConfig.contentName])), config);
+    return (0, quads_1.serialize2quads)(filterObject(obj, new Set([r_bridge_1.attributesKey, r_bridge_1.childrenKey, r_bridge_1.contentKey])), config);
 }
 exports.parseToQuads = parseToQuads;
 //# sourceMappingURL=parse-printer.js.map

package/core/slicer.js

@@ -162,22 +162,18 @@ class SteppingSlicer {
                 break;
             case 1:
                 step = guardStep('normalize');
-                result = await (0, steps_1.executeSingleSubStep)(step, this.results.parse, await this.shell.tokenMap(), this.hooks, this.getId);
+                result = (0, steps_1.executeSingleSubStep)(step, this.results.parse, this.hooks, this.getId);
                 break;
             case 2:
                 step = guardStep('dataflow');
-                result = (0, steps_1.executeSingleSubStep)(step, this.results.normalize);
+                result = (0, steps_1.executeSingleSubStep)(step, this.request, this.results.normalize);
                 break;
             case 3:
-                step = guardStep('ai');
-                result = (0, steps_1.executeSingleSubStep)(step, this.results.normalize, this.results.dataflow);
-                break;
-            case 4:
                 (0, assert_1.guard)(this.criterion !== undefined, 'Cannot decode criteria without a criterion');
                 step = guardStep('slice');
-                result = (0, steps_1.executeSingleSubStep)(step, this.results.ai.graph, this.results.normalize, this.criterion);
+                result = (0, steps_1.executeSingleSubStep)(step, this.results.dataflow.graph, this.results.normalize, this.criterion);
                 break;
-            case 5:
+            case 4:
                 step = guardStep('reconstruct');
                 result = (0, steps_1.executeSingleSubStep)(step, this.results.normalize, this.results.slice.result);
                 break;

package/core/steps.d.ts

@@ -13,15 +13,14 @@
  * @module
  */
 import type { MergeableRecord } from '../util/objects';
-import { normalize, retrieveXmlFromRCode } from '../r-bridge';
-import { produceDataFlowGraph } from '../dataflow';
+import { retrieveParseDataFromRCode } from '../r-bridge';
 import { reconstructToCode, staticSlicing } from '../slicing';
 import type { IStepPrinter } from './print/print';
 import { internalPrinter, StepOutputFormat } from './print/print';
 import { normalizedAstToJson, normalizedAstToQuads, printNormalizedAstToMermaid, printNormalizedAstToMermaidUrl } from './print/normalize-printer';
 import { parseToQuads } from './print/parse-printer';
 import { dataflowGraphToJson, dataflowGraphToMermaid, dataflowGraphToMermaidUrl, dataflowGraphToQuads } from './print/dataflow-printer';
-import type { DataflowInformation } from '../dataflow/internal/info';
+import { normalize } from '../r-bridge/lang-4.x/ast/parser/json/parser';
 /**
  * This represents close a function that we know completely nothing about.
  * Nevertheless, this is the basis of what a step processor should look like.
@@ -49,7 +48,7 @@ export interface IStep<Fn extends StepFunction> extends MergeableRecord {
 export declare const STEPS_PER_FILE: {
     readonly parse: {
         description: string;
-        processor: typeof retrieveXmlFromRCode;
+        processor: typeof retrieveParseDataFromRCode;
         required: "once-per-file";
         printer: {
             0: typeof internalPrinter;
@@ -71,7 +70,7 @@ export declare const STEPS_PER_FILE: {
     };
     readonly dataflow: {
         description: string;
-        processor: typeof produceDataFlowGraph;
+        processor: (r: import("../r-bridge").RParseRequest, a: import("../r-bridge").NormalizedAst<import("../r-bridge").ParentInformation>) => import("../dataflow/internal/info").DataflowInformation;
         required: "once-per-file";
         printer: {
             0: typeof internalPrinter;
@@ -81,14 +80,6 @@ export declare const STEPS_PER_FILE: {
             4: typeof dataflowGraphToMermaidUrl;
         };
     };
-    readonly ai: {
-        description: string;
-        processor: (_: import("../r-bridge").NormalizedAst<import("../r-bridge").ParentInformation>, dfInfo: DataflowInformation) => DataflowInformation;
-        required: "once-per-file";
-        printer: {
-            0: typeof internalPrinter;
-        };
-    };
 };
 export declare const STEPS_PER_SLICE: {
     readonly slice: {
@@ -127,7 +118,7 @@ export declare const STEPS: {
     };
     readonly parse: {
         description: string;
-        processor: typeof retrieveXmlFromRCode;
+        processor: typeof retrieveParseDataFromRCode;
         required: "once-per-file";
         printer: {
             0: typeof internalPrinter;
@@ -149,7 +140,7 @@ export declare const STEPS: {
     };
     readonly dataflow: {
         description: string;
-        processor: typeof produceDataFlowGraph;
+        processor: (r: import("../r-bridge").RParseRequest, a: import("../r-bridge").NormalizedAst<import("../r-bridge").ParentInformation>) => import("../dataflow/internal/info").DataflowInformation;
         required: "once-per-file";
         printer: {
             0: typeof internalPrinter;
@@ -159,16 +150,8 @@ export declare const STEPS: {
             4: typeof dataflowGraphToMermaidUrl;
         };
     };
-    readonly ai: {
-        description: string;
-        processor: (_: import("../r-bridge").NormalizedAst<import("../r-bridge").ParentInformation>, dfInfo: DataflowInformation) => DataflowInformation;
-        required: "once-per-file";
-        printer: {
-            0: typeof internalPrinter;
-        };
-    };
 };
-export declare const LAST_PER_FILE_STEP: "ai";
+export declare const LAST_PER_FILE_STEP: "dataflow";
 export declare const LAST_STEP: "reconstruct";
 export type StepName = keyof typeof STEPS;
 export type Step<Name extends StepName> = typeof STEPS[Name];

package/core/steps.js

@@ -23,10 +23,11 @@ const normalize_printer_1 = require("./print/normalize-printer");
 const assert_1 = require("../util/assert");
 const parse_printer_1 = require("./print/parse-printer");
 const dataflow_printer_1 = require("./print/dataflow-printer");
+const parser_1 = require("../r-bridge/lang-4.x/ast/parser/json/parser");
 exports.STEPS_PER_FILE = {
     'parse': {
         description: 'Parse the given R code into an AST',
-        processor: r_bridge_1.retrieveXmlFromRCode,
+        processor: r_bridge_1.retrieveParseDataFromRCode,
         required: 'once-per-file',
         printer: {
             [0 /* StepOutputFormat.Internal */]: print_1.internalPrinter,
@@ -36,7 +37,7 @@ exports.STEPS_PER_FILE = {
     },
     'normalize': {
         description: 'Normalize the AST to flowR\'s AST (first step of the normalization)',
-        processor: r_bridge_1.normalize,
+        processor: parser_1.normalize,
         required: 'once-per-file',
         printer: {
             [0 /* StepOutputFormat.Internal */]: print_1.internalPrinter,
@@ -48,7 +49,7 @@ exports.STEPS_PER_FILE = {
     },
     'dataflow': {
         description: 'Construct the dataflow graph',
-        processor: dataflow_1.produceDataFlowGraph,
+        processor: (r, a) => (0, dataflow_1.produceDataFlowGraph)(r, a),
         required: 'once-per-file',
         printer: {
             [0 /* StepOutputFormat.Internal */]: print_1.internalPrinter,
@@ -57,14 +58,6 @@ exports.STEPS_PER_FILE = {
             [3 /* StepOutputFormat.Mermaid */]: dataflow_printer_1.dataflowGraphToMermaid,
             [4 /* StepOutputFormat.MermaidUrl */]: dataflow_printer_1.dataflowGraphToMermaidUrl
         }
-    },
-    'ai': {
-        description: 'Run abstract interpretation',
-        processor: (_, dfInfo) => dfInfo, // Use runAbstractInterpretation here when it's ready
-        required: 'once-per-file',
-        printer: {
-            [0 /* StepOutputFormat.Internal */]: print_1.internalPrinter
-        }
     }
 };
 exports.STEPS_PER_SLICE = {
@@ -86,7 +79,7 @@ exports.STEPS_PER_SLICE = {
     }
 };
 exports.STEPS = { ...exports.STEPS_PER_FILE, ...exports.STEPS_PER_SLICE };
-exports.LAST_PER_FILE_STEP = 'ai';
+exports.LAST_PER_FILE_STEP = 'dataflow';
 exports.LAST_STEP = 'reconstruct';
 function executeSingleSubStep(subStep, ...input) {
     // @ts-expect-error - this is safe, as we know that the function arguments are correct by 'satisfies', this saves an explicit cast with 'as'

package/dataflow/environments/environment.js

@@ -77,6 +77,14 @@ exports.DefaultEnvironmentMemory = new Map([
                 definedAt: exports.BuiltIn,
                 name: 'print',
                 nodeId: exports.BuiltIn
+            }]],
+    ['source', [{
+                kind: 'built-in-function',
+                scope: scopes_1.GlobalScope,
+                used: 'always',
+                definedAt: exports.BuiltIn,
+                name: 'source',
+                nodeId: exports.BuiltIn
             }]]
 ]);
 function initializeCleanEnvironments() {

package/dataflow/environments/register.js

@@ -10,6 +10,7 @@ const assert_1 = require("../../util/assert");
  */
 function define(definition, withinScope, environments) {
     let newEnvironments = environments;
+    (0, assert_1.guard)(withinScope === definition.scope, 'Mismatching scopes');
     if (withinScope === scopes_1.LocalScope) {
         newEnvironments = (0, environment_1.cloneEnvironments)(environments, false);
         newEnvironments.current.memory.set(definition.name, [definition]);

package/dataflow/extractor.d.ts

@@ -1,6 +1,6 @@
-import type { NormalizedAst, ParentInformation, RBinaryOp } from '../r-bridge';
+import type { NormalizedAst, ParentInformation, RBinaryOp, RParseRequest } from '../r-bridge';
 import type { DataflowInformation } from './internal/info';
 import type { DataflowProcessorInformation } from './processor';
 import type { DataflowScopeName } from './environments';
-export declare function produceDataFlowGraph<OtherInfo>(ast: NormalizedAst<OtherInfo & ParentInformation>, initialScope?: DataflowScopeName): DataflowInformation;
+export declare function produceDataFlowGraph<OtherInfo>(request: RParseRequest, ast: NormalizedAst<OtherInfo & ParentInformation>, initialScope?: DataflowScopeName): DataflowInformation;
 export declare function processBinaryOp<OtherInfo>(node: RBinaryOp<OtherInfo & ParentInformation>, data: DataflowProcessorInformation<OtherInfo & ParentInformation>): DataflowInformation;