@eagleoutice/flowr 2.0.11 → 2.0.12

package/cli/repl/server/connection.js

@@ -1,4 +1,30 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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.sanitizeAnalysisResults = exports.FlowRServerConnection = void 0;
 const send_1 = require("./send");
@@ -17,6 +43,9 @@ const _10_normalize_1 = require("../../../core/steps/all/core/10-normalize");
 const _20_dataflow_1 = require("../../../core/steps/all/core/20-dataflow");
 const ansi_1 = require("../../../util/ansi");
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
+const graph_1 = require("../../../dataflow/graph/graph");
+const tmp = __importStar(require("tmp"));
+const fs_1 = __importDefault(require("fs"));
 /**
  * Each connection handles a single client, answering to its requests.
  * There is no need to construct this class manually, {@link FlowRServer} will do it for you.
@@ -26,16 +55,18 @@ class FlowRServerConnection {
     shell;
     name;
     logger;
+    allowRSessionAccess;
     // maps token to information
     fileMap = new Map();
     // we do not have to ensure synchronized shell-access as we are always running synchronized
-    constructor(socket, name, shell) {
+    constructor(socket, name, shell, allowRSessionAccess) {
         this.socket = socket;
         this.shell = shell;
         this.name = name;
         this.logger = server_1.serverLog.getSubLogger({ name });
         this.socket.on('data', data => this.handleData(String(data)));
         this.socket.on('error', e => this.logger.error(`[${this.name}] Error while handling connection: ${String(e)}`));
+        this.allowRSessionAccess = allowRSessionAccess;
     }
     currentMessageBuffer = '';
     handleData(message) {
@@ -56,7 +87,7 @@ class FlowRServerConnection {
         }
         switch (request.message.type) {
             case 'request-file-analysis':
-                this.handleFileAnalysisRequest(request.message);
+                void this.handleFileAnalysisRequest(request.message);
                 break;
             case 'request-slice':
                 this.handleSliceRequest(request.message);
@@ -74,7 +105,7 @@ class FlowRServerConnection {
                 this.socket.end();
         }
     }
-    handleFileAnalysisRequest(base) {
+    async handleFileAnalysisRequest(base) {
         const requestResult = (0, validate_1.validateMessage)(base, analysis_1.requestAnalysisMessage);
         if (requestResult.type === 'error') {
             (0, validate_1.answerForValidationError)(this.socket, requestResult, base.id);
@@ -85,8 +116,9 @@ class FlowRServerConnection {
         if (message.filetoken && this.fileMap.has(message.filetoken)) {
             this.logger.warn(`File token ${message.filetoken} already exists. Overwriting.`);
         }
-        const slicer = this.createPipelineExecutorForRequest(message);
-        void slicer.allRemainingSteps(false).then(async (results) => await this.sendFileAnalysisResponse(results, message))
+        const tempFile = tmp.fileSync({ postfix: '.R' });
+        const slicer = this.createPipelineExecutorForRequest(message, tempFile.name);
+        await slicer.allRemainingSteps(false).then(async (results) => await this.sendFileAnalysisResponse(results, message))
             .catch(e => {
             this.logger.error(`[${this.name}] Error while analyzing file ${message.filename ?? 'unknown file'}: ${String(e)}`);
             (0, send_1.sendMessage)(this.socket, {
@@ -96,6 +128,8 @@ class FlowRServerConnection {
                 reason: `Error while analyzing file ${message.filename ?? 'unknown file'}: ${String(e)}`
             });
         });
+        // this is an interestingly named function that means "I am a callback that removes a file" - so this deletes the file
+        tempFile.removeCallback();
     }
     async sendFileAnalysisResponse(results, message) {
         let cfg = undefined;
@@ -127,14 +161,27 @@ class FlowRServerConnection {
             });
         }
     }
-    createPipelineExecutorForRequest(message) {
+    createPipelineExecutorForRequest(message, tempFile) {
+        let request;
+        if (message.content !== undefined) {
+            // we store the code in a temporary file in case it's too big for the shell to handle
+            fs_1.default.writeFileSync(tempFile, message.content ?? '');
+            request = { request: 'file', content: tempFile };
+        }
+        else if (message.filepath !== undefined) {
+            if (typeof message.filepath === 'string') {
+                request = { request: 'file', content: message.filepath };
+            }
+            else {
+                request = message.filepath.map(fp => ({ request: 'file', content: fp }));
+            }
+        }
+        else {
+            throw new Error('Either content or filepath must be defined.');
+        }
         const slicer = new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_SLICING_PIPELINE, {
             shell: this.shell,
-            // 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
-            },
+            request,
             criterion: [] // currently unknown
         });
         if (message.filetoken) {
@@ -201,7 +248,7 @@ class FlowRServerConnection {
             formatter: request.ansi ? ansi_1.ansiFormatter : ansi_1.voidFormatter,
             stdout: msg => out('stdout', msg),
             stderr: msg => out('stderr', msg)
-        }, request.expression, this.shell).then(() => {
+        }, request.expression, this.shell, this.allowRSessionAccess).then(() => {
             (0, send_1.sendMessage)(this.socket, {
                 type: 'end-repl-execution',
                 id: request.id
@@ -219,12 +266,8 @@ function sanitizeAnalysisResults(results) {
         },
         dataflow: {
             ...results.dataflow,
-            graph: {
-                ...results.dataflow?.graph,
-                functionCache: undefined,
-                // @ts-expect-error this is private, but we want to sanitize it for the purpose of json serialization
-                _idMap: undefined
-            }
+            // we want to keep the DataflowGraph type information, but not the idMap
+            graph: new graph_1.DataflowGraph(undefined).mergeWith(results.dataflow?.graph)
         }
     };
 }

package/cli/repl/server/messages/analysis.d.ts

@@ -12,7 +12,7 @@ export interface FileAnalysisRequestMessage extends IdMessageBase {
      * This is a unique token that you assign to subsequently slice the respective files.
      * If you pass the same token multiple times, previous results will be overwritten.
      *
-     * If you do not pass a file token, the server will _not_ store the results!
+     * If you do _not_ pass a file token, the server will _not_ store the results!
      */
     filetoken?: string;
     /**
@@ -20,10 +20,16 @@ export interface FileAnalysisRequestMessage extends IdMessageBase {
      * However, the name is only for debugging and bears no semantic meaning.
      */
     filename?: string;
-    /** The contents of the file, or an R expression itself (like `1 + 1`), give either this or the `filepath`. */
+    /**
+     * The contents of the file, or an R expression itself (like `1 + 1`), give either this or the `filepath`.
+     * If you want to load multiple R files as one, either use `filepath` or concatenate the file-contents for this field.
+     */
     content?: string;
-    /** The filepath on the local machine, accessible to flowR, or simply. Give either this or the `content` */
-    filepath?: string;
+    /**
+     * The filepath on the local machine, accessible to flowR, or simply. Give either this or the `content`.
+     * If you want to load multiple R files as one, either use this or concatenate the file-contents for the `content`.
+     */
+    filepath?: string | readonly string[];
     /** Can be used to additionally extract the {@link ControlFlowInformation} of the file, which is not exposed (and not fully calculated) by default. */
     cfg?: boolean;
     /** Controls the serialization of the `results` (and the {@link ControlFlowGraph} if the corresponding flag is set). If missing, we assume _json_. */
@@ -35,7 +41,7 @@ export declare const requestAnalysisMessage: MessageDefinition<FileAnalysisReque
  * It contains the results of the analysis in JSON format (guided by {@link FileAnalysisRequestMessage#format}).
  *
  * The `idMap` of the normalization step (see {@link NormalizedAst}) is not serialized as it would essentially
- * repeat the complete normalized AST.
+ * repeat the complete normalized AST, you have to re-create it yourself if you require it.
  *
  * @note The serialization of maps and sets is controlled by the {@link jsonReplacer} as part of {@link sendMessage}.
  *

package/cli/repl/server/messages/analysis.js

@@ -13,7 +13,7 @@ exports.requestAnalysisMessage = {
         filetoken: joi_1.default.string().optional(),
         filename: joi_1.default.string().optional(),
         content: joi_1.default.string().optional(),
-        filepath: joi_1.default.string().optional(),
+        filepath: joi_1.default.alternatives(joi_1.default.string(), joi_1.default.array().items(joi_1.default.string())).optional(),
         cfg: joi_1.default.boolean().optional(),
         format: joi_1.default.string().valid('json', 'n-quads').optional()
     }).xor('content', 'filepath')

package/cli/repl/server/server.d.ts

@@ -11,10 +11,11 @@ export declare class FlowRServer {
     private readonly server;
     private readonly shell;
     private versionInformation;
+    private allowRSessionAccess;
     /** maps names to the respective connection */
     private connections;
     private nameCounter;
-    constructor(shell: RShell, server?: Server);
+    constructor(shell: RShell, allowRSessionAccess: boolean, server?: Server);
     start(port: number): Promise<void>;
     private onConnect;
 }

package/cli/repl/server/server.js

@@ -17,13 +17,15 @@ class FlowRServer {
     server;
     shell;
     versionInformation;
+    allowRSessionAccess = false;
     /** maps names to the respective connection */
     connections = new Map();
     nameCounter = 0;
-    constructor(shell, server = new net_1.NetServer()) {
+    constructor(shell, allowRSessionAccess, server = new net_1.NetServer()) {
         this.server = server;
         this.server.onConnect(c => this.onConnect(c));
         this.shell = shell;
+        this.allowRSessionAccess = allowRSessionAccess;
     }
     async start(port) {
         this.versionInformation = await (0, version_1.retrieveVersionInformation)(this.shell);
@@ -37,7 +39,7 @@ class FlowRServer {
         }
         const name = `client-${this.nameCounter++}`;
         exports.serverLog.info(`Client connected: ${(0, send_1.getUnnamedSocketName)(c)} as "${name}"`);
-        this.connections.set(name, new connection_1.FlowRServerConnection(c, name, this.shell));
+        this.connections.set(name, new connection_1.FlowRServerConnection(c, name, this.shell, this.allowRSessionAccess));
         helloClient(c, name, this.versionInformation);
         c.on('close', () => {
             this.connections.delete(name);

package/core/steps/all/core/00-parse.d.ts

@@ -3,14 +3,14 @@ import { parseToQuads } from '../../../print/parse-printer';
 import { PipelineStepStage } from '../../pipeline-step';
 import type { RShellExecutor } from '../../../../r-bridge/shell-executor';
 import type { RShell } from '../../../../r-bridge/shell';
-import type { RParseRequest } from '../../../../r-bridge/retriever';
+import type { RParseRequests } from '../../../../r-bridge/retriever';
 export interface ParseRequiredInput {
     /** This is the {@link RShell} or {@link RShellExecutor} connection to be used to obtain the original parses AST of the R code */
     readonly shell: RShell | RShellExecutor;
     /** The request which essentially indicates the input to extract the AST from */
-    readonly request: RParseRequest;
+    readonly request: RParseRequests;
 }
-declare function processor(_results: unknown, input: Partial<ParseRequiredInput>): import("ts-essentials").AsyncOrSync<string>;
+declare function processor(_results: unknown, input: Partial<ParseRequiredInput>): Promise<string>;
 export declare const PARSE_WITH_R_SHELL_STEP: {
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";

package/core/steps/all/core/00-parse.js

@@ -5,7 +5,13 @@ const print_1 = require("../../../print/print");
 const parse_printer_1 = require("../../../print/parse-printer");
 const retriever_1 = require("../../../../r-bridge/retriever");
 function processor(_results, input) {
-    return (0, retriever_1.retrieveParseDataFromRCode)(input.request, input.shell);
+    /* in the future, we want to expose all cases */
+    if (Array.isArray(input.request)) {
+        return (0, retriever_1.retrieveParseDataFromRCode)(input.request[0], input.shell);
+    }
+    else {
+        return (0, retriever_1.retrieveParseDataFromRCode)(input.request, input.shell);
+    }
 }
 exports.PARSE_WITH_R_SHELL_STEP = {
     name: 'parse',

package/core/steps/all/core/20-dataflow.d.ts

@@ -2,11 +2,11 @@ import { internalPrinter } from '../../../print/print';
 import { PipelineStepStage } from '../../pipeline-step';
 import { dataflowGraphToJson, dataflowGraphToMermaid, dataflowGraphToMermaidUrl, dataflowGraphToQuads } from '../../../print/dataflow-printer';
 import type { NormalizedAst } from '../../../../r-bridge/lang-4.x/ast/model/processing/decorate';
-import type { RParseRequest } from '../../../../r-bridge/retriever';
+import type { RParseRequests } from '../../../../r-bridge/retriever';
 declare function legacyProcessor(results: {
     normalize?: NormalizedAst;
 }, input: {
-    request?: RParseRequest;
+    request?: RParseRequests;
 }): import("../../../../dataflow/info").DataflowInformation;
 export declare const STATIC_DATAFLOW: {
     readonly humanReadableName: "dataflow";

package/core/steps/pipeline/default-pipelines.d.ts

@@ -2,7 +2,7 @@ export declare const DEFAULT_SLICING_PIPELINE: import("./pipeline").Pipeline<{
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
     readonly description: "Parse the given R code into an AST";
-    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => import("ts-essentials").AsyncOrSync<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
@@ -33,7 +33,7 @@ export declare const DEFAULT_SLICING_PIPELINE: import("./pipeline").Pipeline<{
     readonly processor: (results: {
         normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>> | undefined;
     }, input: {
-        request?: import("../../../r-bridge/retriever").RParseRequest | undefined;
+        request?: import("../../../r-bridge/retriever").RParseRequests | undefined;
     }) => import("../../../dataflow/info").DataflowInformation;
     readonly requiredInput: {};
     readonly name: "dataflow";
@@ -80,7 +80,7 @@ export declare const DEFAULT_RECONSTRUCT_PIPELINE: import("./pipeline").Pipeline
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
     readonly description: "Parse the given R code into an AST";
-    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => import("ts-essentials").AsyncOrSync<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
@@ -111,7 +111,7 @@ export declare const DEFAULT_RECONSTRUCT_PIPELINE: import("./pipeline").Pipeline
     readonly processor: (results: {
         normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>> | undefined;
     }, input: {
-        request?: import("../../../r-bridge/retriever").RParseRequest | undefined;
+        request?: import("../../../r-bridge/retriever").RParseRequests | undefined;
     }) => import("../../../dataflow/info").DataflowInformation;
     readonly requiredInput: {};
     readonly name: "dataflow";
@@ -158,7 +158,7 @@ export declare const DEFAULT_DATAFLOW_PIPELINE: import("./pipeline").Pipeline<{
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
     readonly description: "Parse the given R code into an AST";
-    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => import("ts-essentials").AsyncOrSync<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
@@ -189,7 +189,7 @@ export declare const DEFAULT_DATAFLOW_PIPELINE: import("./pipeline").Pipeline<{
     readonly processor: (results: {
         normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>> | undefined;
     }, input: {
-        request?: import("../../../r-bridge/retriever").RParseRequest | undefined;
+        request?: import("../../../r-bridge/retriever").RParseRequests | undefined;
     }) => import("../../../dataflow/info").DataflowInformation;
     readonly requiredInput: {};
     readonly name: "dataflow";
@@ -208,7 +208,7 @@ export declare const DEFAULT_NORMALIZE_PIPELINE: import("./pipeline").Pipeline<{
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
     readonly description: "Parse the given R code into an AST";
-    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => import("ts-essentials").AsyncOrSync<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
@@ -239,7 +239,7 @@ export declare const DEFAULT_PARSE_PIPELINE: import("./pipeline").Pipeline<{
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
     readonly description: "Parse the given R code into an AST";
-    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => import("ts-essentials").AsyncOrSync<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;

package/dataflow/environments/built-in.js

@@ -108,7 +108,7 @@ registerBuiltInFunctions(true, ['return'], defaultBuiltInProcessor, { returnsNth
 registerBuiltInFunctions(true, ['break'], defaultBuiltInProcessor, { cfg: 2 /* ExitPointType.Break */ });
 registerBuiltInFunctions(true, ['next'], defaultBuiltInProcessor, { cfg: 3 /* ExitPointType.Next */ });
 registerBuiltInFunctions(true, ['{'], built_in_expression_list_1.processExpressionList, {});
-registerBuiltInFunctions(true, ['source'], built_in_source_1.processSourceCall, {});
+registerBuiltInFunctions(true, ['source'], built_in_source_1.processSourceCall, { includeFunctionCall: true, forceFollow: false });
 registerBuiltInFunctions(true, ['[', '[['], built_in_access_1.processAccess, { treatIndicesAsString: false });
 registerBuiltInFunctions(true, ['$', '@'], built_in_access_1.processAccess, { treatIndicesAsString: true });
 registerBuiltInFunctions(true, ['if', 'ifelse'], built_in_if_then_else_1.processIfThenElse, {});

package/dataflow/extractor.d.ts

@@ -1,6 +1,6 @@
 import type { DataflowInformation } from './info';
 import type { DataflowProcessors } from './processor';
 import type { NormalizedAst, ParentInformation } from '../r-bridge/lang-4.x/ast/model/processing/decorate';
-import type { RParseRequest } from '../r-bridge/retriever';
+import type { RParseRequests } from '../r-bridge/retriever';
 export declare const processors: DataflowProcessors<ParentInformation>;
-export declare function produceDataFlowGraph<OtherInfo>(request: RParseRequest, ast: NormalizedAst<OtherInfo & ParentInformation>): DataflowInformation;
+export declare function produceDataFlowGraph<OtherInfo>(request: RParseRequests, ast: NormalizedAst<OtherInfo & ParentInformation>): DataflowInformation;

package/dataflow/extractor.js

@@ -14,6 +14,7 @@ const make_argument_1 = require("./internal/process/functions/call/argument/make
 const range_1 = require("../util/range");
 const retriever_1 = require("../r-bridge/retriever");
 const environment_1 = require("./environments/environment");
+const built_in_source_1 = require("./internal/process/functions/call/built-in/built-in-source");
 exports.processors = {
     ["RNumber" /* RType.Number */]: process_value_1.processValue,
     ["RString" /* RType.String */]: process_value_1.processValue,
@@ -45,14 +46,29 @@ exports.processors = {
     }, (0, make_argument_1.wrapArgumentsUnnamed)(n.children, d.completeAst.idMap), n.info.id, d)
 };
 function produceDataFlowGraph(request, ast) {
-    return (0, processor_1.processDataflowFor)(ast.ast, {
+    const multifile = Array.isArray(request);
+    let firstRequest;
+    if (multifile) {
+        firstRequest = request[0];
+    }
+    else {
+        firstRequest = request;
+    }
+    const dfData = {
         completeAst: ast,
         environment: (0, environment_1.initializeCleanEnvironments)(),
         processors: exports.processors,
-        currentRequest: request,
+        currentRequest: firstRequest,
         controlDependencies: undefined,
-        referenceChain: [(0, retriever_1.requestFingerprint)(request)]
-    });
+        referenceChain: [(0, retriever_1.requestFingerprint)(firstRequest)]
+    };
+    let df = (0, processor_1.processDataflowFor)(ast.ast, dfData);
+    if (multifile) {
+        for (let i = 1; i < request.length; i++) {
+            df = (0, built_in_source_1.standaloneSourceFile)(request[i], dfData, `root-${i}`, df);
+        }
+    }
+    return df;
 }
 exports.produceDataFlowGraph = produceDataFlowGraph;
 //# sourceMappingURL=extractor.js.map

package/dataflow/info.d.ts

@@ -5,25 +5,31 @@ import type { REnvironmentInformation } from './environments/environment';
 import { DataflowGraph } from './graph/graph';
 import type { GenericDifferenceInformation, WriteableDifferenceReport } from '../util/diff';
 export declare const enum ExitPointType {
+    /** The exit point is the implicit (last executed expression of a function/block) */
     Default = 0,
+    /** The exit point is an explicit `return` call (or an alias of it) */
     Return = 1,
+    /** The exit point is an explicit `break` call (or an alias of it) */
     Break = 2,
+    /** The exit point is an explicit `next` call (or an alias of it) */
     Next = 3
 }
 export interface ControlDependency {
+    /** The id of the node that causes the control dependency to be active (e.g., the condition of an if) */
     readonly id: NodeId;
     /** when does this control dependency trigger (if the condition is true or false)? */
     readonly when?: boolean;
 }
 export interface ExitPoint {
+    /** What kind of exit point is this one? May be used to filter for exit points of specific causes. */
     readonly type: ExitPointType;
+    /** The id of the node which causes the exit point! */
     readonly nodeId: NodeId;
+    /** Control dependencies which influence if the exit point triggers (e.g., if the `return` is contained within an `if` statement) */
     readonly controlDependencies: ControlDependency[] | undefined;
 }
 export declare function addNonDefaultExitPoints(existing: ExitPoint[], add: readonly ExitPoint[]): void;
-/**
- * The control flow information for the current {@link DataflowInformation}.
- */
+/** The control flow information for the current {@link DataflowInformation}. */
 export interface DataflowCfgInformation {
     /**
      * The entry node into the subgraph

package/dataflow/internal/process/functions/call/built-in/built-in-source.d.ts

@@ -1,11 +1,17 @@
 import { type DataflowProcessorInformation } from '../../../../../processor';
 import type { DataflowInformation } from '../../../../../info';
-import type { RParseRequest, RParseRequestProvider } from '../../../../../../r-bridge/retriever';
+import type { RParseRequestProvider, RParseRequest } from '../../../../../../r-bridge/retriever';
 import type { IdGenerator, ParentInformation } from '../../../../../../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { RFunctionArgument } from '../../../../../../r-bridge/lang-4.x/ast/model/nodes/r-function-call';
 import type { RSymbol } from '../../../../../../r-bridge/lang-4.x/ast/model/nodes/r-symbol';
 import type { NodeId } from '../../../../../../r-bridge/lang-4.x/ast/model/processing/node-id';
 import type { NoInfo } from '../../../../../../r-bridge/lang-4.x/ast/model/model';
 export declare function setSourceProvider(provider: RParseRequestProvider): void;
-export declare function processSourceCall<OtherInfo>(name: RSymbol<OtherInfo & ParentInformation>, args: readonly RFunctionArgument<OtherInfo & ParentInformation>[], rootId: NodeId, data: DataflowProcessorInformation<OtherInfo & ParentInformation>): DataflowInformation;
+export declare function processSourceCall<OtherInfo>(name: RSymbol<OtherInfo & ParentInformation>, args: readonly RFunctionArgument<OtherInfo & ParentInformation>[], rootId: NodeId, data: DataflowProcessorInformation<OtherInfo & ParentInformation>, config: {
+    /** should this produce an explicit source function call in the graph? */
+    includeFunctionCall?: boolean;
+    /** should this function call be followed, even when the configuratio disables it? */
+    forceFollow?: boolean;
+}): DataflowInformation;
 export declare function sourceRequest<OtherInfo>(request: RParseRequest, data: DataflowProcessorInformation<OtherInfo & ParentInformation>, information: DataflowInformation, getId: IdGenerator<NoInfo>): DataflowInformation;
+export declare function standaloneSourceFile<OtherInfo>(inputRequest: RParseRequest, data: DataflowProcessorInformation<OtherInfo & ParentInformation>, uniqueSourceId: string, information: DataflowInformation): DataflowInformation;

package/dataflow/internal/process/functions/call/built-in/built-in-source.js

@@ -1,8 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.sourceRequest = exports.processSourceCall = exports.setSourceProvider = void 0;
+exports.standaloneSourceFile = exports.sourceRequest = exports.processSourceCall = exports.setSourceProvider = void 0;
 const shell_executor_1 = require("../../../../../../r-bridge/shell-executor");
 const processor_1 = require("../../../../../processor");
+const info_1 = require("../../../../../info");
 const config_1 = require("../../../../../../config");
 const parser_1 = require("../../../../../../r-bridge/lang-4.x/ast/parser/json/parser");
 const known_call_handling_1 = require("../known-call-handling");
@@ -16,10 +17,12 @@ function setSourceProvider(provider) {
     sourceProvider = provider;
 }
 exports.setSourceProvider = setSourceProvider;
-function processSourceCall(name, args, rootId, data) {
-    const information = (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data }).information;
+function processSourceCall(name, args, rootId, data, config) {
+    const information = config.includeFunctionCall ?
+        (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data }).information
+        : (0, info_1.initializeCleanDataflowInformation)(rootId, data);
     const sourceFile = args[0];
-    if ((0, config_1.getConfig)().ignoreSourceCalls) {
+    if (!config.forceFollow && (0, config_1.getConfig)().ignoreSourceCalls) {
         logger_1.dataflowLogger.info(`Skipping source call ${JSON.stringify(sourceFile)} (disabled in config file)`);
         return information;
     }
@@ -69,4 +72,22 @@ function sourceRequest(request, data, information, getId) {
     return newInformation;
 }
 exports.sourceRequest = sourceRequest;
+function standaloneSourceFile(inputRequest, data, uniqueSourceId, information) {
+    const path = inputRequest.request === 'file' ? inputRequest.content : '-inline-';
+    /* this way we can still pass content */
+    const request = inputRequest.request === 'file' ? sourceProvider.createRequest(inputRequest.content) : inputRequest;
+    const fingerprint = (0, retriever_1.requestFingerprint)(request);
+    // check if the sourced file has already been dataflow analyzed, and if so, skip it
+    if (data.referenceChain.includes(fingerprint)) {
+        logger_1.dataflowLogger.info(`Found loop in dataflow analysis for ${JSON.stringify(request)}: ${JSON.stringify(data.referenceChain)}, skipping further dataflow analysis`);
+        return information;
+    }
+    return sourceRequest(request, {
+        ...data,
+        currentRequest: request,
+        environment: information.environment,
+        referenceChain: [...data.referenceChain, fingerprint]
+    }, information, (0, decorate_1.deterministicPrefixIdGenerator)(path + '@' + uniqueSourceId));
+}
+exports.standaloneSourceFile = standaloneSourceFile;
 //# sourceMappingURL=built-in-source.js.map

package/dataflow/processor.d.ts

@@ -21,11 +21,11 @@ export interface DataflowProcessorInformation<OtherInfo> {
    */
     readonly processors: DataflowProcessors<OtherInfo>;
     /**
-     * The {@link RParseRequest} that is currently being parsed
+     * The {@link RParseRequests} that is currently being parsed
      */
     readonly currentRequest: RParseRequest;
     /**
-     * The chain of {@link RParseRequest} fingerprints ({@link requestFingerprint}) that lead to the {@link currentRequest}.
+     * The chain of {@link RParseRequests} fingerprints ({@link requestFingerprint}) that lead to the {@link currentRequest}.
      * The most recent (last) entry is expected to always be the {@link currentRequest}.
      */
     readonly referenceChain: string[];
@@ -47,11 +47,12 @@ export type DataflowProcessors<OtherInfo> = {
 /**
  * Originally, dataflow processor was written as a two-way fold, but this produced problems when trying to resolve function calls
  * which require information regarding the calling *and* definition context. While this only is a problem for late bindings as they happen
- * with functions (and probably quote'd R-expressions) it is still a problem that must be dealt with.
+ * with functions (and probably quote'd R-expressions), it is still a problem that must be dealt with.
  * Therefore, the dataflow processor has no complete control over the traversal and merge strategy of the graph, with each processor being in
  * the position to call the other processors as needed for its children.
  * <p>
- * Now this method can be called recursively within the other processors to parse the dataflow for nodes that you can not narrow down.
+ * Now this method can be called recursively within the other processors to parse the dataflow for nodes that you cannot narrow down
+ * in type or context.
  *
  * @param current - The current node to start processing from
  * @param data    - The initial (/current) information to be passed down

package/dataflow/processor.js

@@ -4,11 +4,12 @@ exports.processDataflowFor = void 0;
 /**
  * Originally, dataflow processor was written as a two-way fold, but this produced problems when trying to resolve function calls
  * which require information regarding the calling *and* definition context. While this only is a problem for late bindings as they happen
- * with functions (and probably quote'd R-expressions) it is still a problem that must be dealt with.
+ * with functions (and probably quote'd R-expressions), it is still a problem that must be dealt with.
  * Therefore, the dataflow processor has no complete control over the traversal and merge strategy of the graph, with each processor being in
  * the position to call the other processors as needed for its children.
  * <p>
- * Now this method can be called recursively within the other processors to parse the dataflow for nodes that you can not narrow down.
+ * Now this method can be called recursively within the other processors to parse the dataflow for nodes that you cannot narrow down
+ * in type or context.
  *
  * @param current - The current node to start processing from
  * @param data    - The initial (/current) information to be passed down

package/package.json

@@ -1,18 +1,20 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.0.11",
+  "version": "2.0.12",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {
     "type": "git",
-    "url": "git+https://github.com/Code-Inspect/flowr.git"
+    "url": "git+https://github.com/flowr-analysis/flowr.git"
   },
-  "homepage": "https://github.com/Code-Inspect/flowr",
+  "homepage": "https://github.com/flowr-analysis/flowr",
   "bugs": {
-    "url": "https://github.com/Code-Inspect/flowr/issues"
+    "url": "https://github.com/flowr-analysis/flowr/issues"
   },
   "scripts": {
     "main": "npm run build:bundle-flowr && node dist/src/cli/flowr.min.js",
+    "flowr": "npm run main --",
+    "main-dev": "ts-node src/cli/flowr.ts",
     "publish-library": "cp .npmignore package.json README.md LICENSE dist/src/ && cd dist/src && npm publish --access public",
     "release": "npx release-it --ci",
     "stats": "ts-node src/cli/statistics-app.ts",
@@ -94,7 +96,7 @@
     ],
     "entryPoints": [
       "src",
-      "test/helper"
+      "test/functionality/_helper"
     ],
     "entryPointStrategy": "expand",
     "exclude": [

package/r-bridge/data/types.d.ts

@@ -1,7 +1,7 @@
 declare const enum RequiredFeature {
-    /** https://github.com/Code-Inspect/flowr/labels/typing */
+    /** https://github.com/flowr-analysis/flowr/labels/typing */
     Typing = 0,
-    /** https://github.com/Code-Inspect/flowr/labels/abstract%20interpretation */
+    /** https://github.com/flowr-analysis/flowr/labels/abstract%20interpretation */
     AbstractInterpretation = 1
 }
 export interface FlowrCapability {