@eagleoutice/flowr 2.2.1 → 2.2.2

package/cli/flowr.js

@@ -23,6 +23,7 @@ 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"));
+const path_1 = __importDefault(require("path"));
 exports.toolName = 'flowr';
 exports.optionHelp = [
     {
@@ -63,7 +64,7 @@ if (options['config-json']) {
 if (!usedConfig) {
     if (options['config-file']) {
         // validate it exists
-        if (!fs_1.default.existsSync(options['config-file'])) {
+        if (!fs_1.default.existsSync(path_1.default.resolve(options['config-file']))) {
             log_1.log.error(`Config file '${options['config-file']}' does not exist`);
             process.exit(1);
         }

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

@@ -1,24 +1,41 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.controlflowStarCommand = exports.controlflowCommand = void 0;
 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");
+const ansi_1 = require("../../../util/ansi");
+const clipboardy_1 = __importDefault(require("clipboardy"));
 async function controlflow(parser, remainingLine) {
-    return await (0, default_pipelines_1.createNormalizePipeline)(parser, {
+    return await (0, default_pipelines_1.createDataflowPipeline)(parser, {
         request: (0, retriever_1.requestFromInput)(remainingLine.trim())
     }).allRemainingSteps();
 }
+function handleString(code) {
+    return code.startsWith('"') ? JSON.parse(code) : code;
+}
+function formatInfo(out, type) {
+    return out.formatter.format(`Copied ${type} to clipboard.`, { color: 7 /* Colors.White */, effect: ansi_1.ColorEffect.Foreground, style: 3 /* FontStyles.Italic */ });
+}
 exports.controlflowCommand = {
     description: `Get mermaid code for the control-flow graph of R code, start with '${retriever_1.fileProtocol}' to indicate a file`,
     usageExample: ':controlflow',
     aliases: ['cfg', 'cf'],
     script: false,
     fn: async (output, shell, remainingLine) => {
-        const result = await controlflow(shell, remainingLine);
-        const cfg = (0, cfg_1.extractCFG)(result.normalize);
-        output.stdout((0, cfg_2.cfgToMermaid)(cfg, result.normalize));
+        const result = await controlflow(shell, handleString(remainingLine));
+        const cfg = (0, cfg_1.extractCFG)(result.normalize, result.dataflow.graph);
+        const mermaid = (0, cfg_2.cfgToMermaid)(cfg, result.normalize);
+        output.stdout(mermaid);
+        try {
+            clipboardy_1.default.writeSync(mermaid);
+            output.stdout(formatInfo(output, 'mermaid code'));
+        }
+        catch (e) { /* do nothing this is a service thing */ }
     }
 };
 exports.controlflowStarCommand = {
@@ -27,9 +44,15 @@ exports.controlflowStarCommand = {
     aliases: ['cfg*', 'cf*'],
     script: false,
     fn: async (output, shell, remainingLine) => {
-        const result = await controlflow(shell, remainingLine);
-        const cfg = (0, cfg_1.extractCFG)(result.normalize);
-        output.stdout((0, cfg_2.cfgToMermaidUrl)(cfg, result.normalize));
+        const result = await controlflow(shell, handleString(remainingLine));
+        const cfg = (0, cfg_1.extractCFG)(result.normalize, result.dataflow.graph);
+        const mermaid = (0, cfg_2.cfgToMermaidUrl)(cfg, result.normalize);
+        output.stdout(mermaid);
+        try {
+            clipboardy_1.default.writeSync(mermaid);
+            output.stdout(formatInfo(output, 'mermaid url'));
+        }
+        catch (e) { /* do nothing this is a service thing */ }
     }
 };
 //# sourceMappingURL=repl-cfg.js.map

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

@@ -1,9 +1,14 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.dataflowStarCommand = exports.dataflowCommand = void 0;
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../../r-bridge/retriever");
 const dfg_1 = require("../../../util/mermaid/dfg");
+const clipboardy_1 = __importDefault(require("clipboardy"));
+const ansi_1 = require("../../../util/ansi");
 async function dataflow(parser, remainingLine) {
     return await (0, default_pipelines_1.createDataflowPipeline)(parser, {
         request: (0, retriever_1.requestFromInput)(remainingLine.trim())
@@ -12,6 +17,9 @@ async function dataflow(parser, remainingLine) {
 function handleString(code) {
     return code.startsWith('"') ? JSON.parse(code) : code;
 }
+function formatInfo(out, type, timing) {
+    return out.formatter.format(`Copied ${type} to clipboard (dataflow: ${timing}ms).`, { color: 7 /* Colors.White */, effect: ansi_1.ColorEffect.Foreground, style: 3 /* FontStyles.Italic */ });
+}
 exports.dataflowCommand = {
     description: `Get mermaid code for the dataflow graph of R code, start with '${retriever_1.fileProtocol}' to indicate a file`,
     usageExample: ':dataflow',
@@ -19,7 +27,13 @@ exports.dataflowCommand = {
     script: false,
     fn: async (output, shell, remainingLine) => {
         const result = await dataflow(shell, handleString(remainingLine));
-        output.stdout((0, dfg_1.graphToMermaid)({ graph: result.dataflow.graph, includeEnvironments: false }).string);
+        const mermaid = (0, dfg_1.graphToMermaid)({ graph: result.dataflow.graph, includeEnvironments: false }).string;
+        output.stdout(mermaid);
+        try {
+            clipboardy_1.default.writeSync(mermaid);
+            output.stdout(formatInfo(output, 'mermaid code', result.dataflow['.meta'].timing));
+        }
+        catch (e) { /* do nothing this is a service thing */ }
     }
 };
 exports.dataflowStarCommand = {
@@ -29,7 +43,13 @@ exports.dataflowStarCommand = {
     script: false,
     fn: async (output, shell, remainingLine) => {
         const result = await dataflow(shell, handleString(remainingLine));
-        output.stdout((0, dfg_1.graphToMermaidUrl)(result.dataflow.graph, false));
+        const mermaid = (0, dfg_1.graphToMermaidUrl)(result.dataflow.graph, false);
+        output.stdout(mermaid);
+        try {
+            clipboardy_1.default.writeSync(mermaid);
+            output.stdout(formatInfo(output, 'mermaid url', result.dataflow['.meta'].timing));
+        }
+        catch (e) { /* do nothing this is a service thing */ }
     }
 };
 //# sourceMappingURL=repl-dataflow.js.map

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

@@ -1,9 +1,14 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.normalizeStarCommand = exports.normalizeCommand = void 0;
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../../r-bridge/retriever");
 const ast_1 = require("../../../util/mermaid/ast");
+const clipboardy_1 = __importDefault(require("clipboardy"));
+const ansi_1 = require("../../../util/ansi");
 async function normalize(parser, remainingLine) {
     return await (0, default_pipelines_1.createNormalizePipeline)(parser, {
         request: (0, retriever_1.requestFromInput)(remainingLine.trim())
@@ -12,6 +17,9 @@ async function normalize(parser, remainingLine) {
 function handleString(code) {
     return code.startsWith('"') ? JSON.parse(code) : code;
 }
+function formatInfo(out, type, timing) {
+    return out.formatter.format(`Copied ${type} to clipboard (normalize: ${timing}ms).`, { color: 7 /* Colors.White */, effect: ansi_1.ColorEffect.Foreground, style: 3 /* FontStyles.Italic */ });
+}
 exports.normalizeCommand = {
     description: `Get mermaid code for the normalized AST of R code, start with '${retriever_1.fileProtocol}' to indicate a file`,
     usageExample: ':normalize',
@@ -19,7 +27,13 @@ exports.normalizeCommand = {
     script: false,
     fn: async (output, shell, remainingLine) => {
         const result = await normalize(shell, handleString(remainingLine));
-        output.stdout((0, ast_1.normalizedAstToMermaid)(result.normalize.ast));
+        const mermaid = (0, ast_1.normalizedAstToMermaid)(result.normalize.ast);
+        output.stdout(mermaid);
+        try {
+            clipboardy_1.default.writeSync(mermaid);
+            output.stdout(formatInfo(output, 'mermaid url', result.normalize['.meta'].timing));
+        }
+        catch (e) { /* do nothing this is a service thing */ }
     }
 };
 exports.normalizeStarCommand = {
@@ -29,7 +43,13 @@ exports.normalizeStarCommand = {
     script: false,
     fn: async (output, shell, remainingLine) => {
         const result = await normalize(shell, handleString(remainingLine));
-        output.stdout((0, ast_1.normalizedAstToMermaidUrl)(result.normalize.ast));
+        const mermaid = (0, ast_1.normalizedAstToMermaidUrl)(result.normalize.ast);
+        output.stdout(mermaid);
+        try {
+            clipboardy_1.default.writeSync(mermaid);
+            output.stdout(formatInfo(output, 'mermaid url', result.normalize['.meta'].timing));
+        }
+        catch (e) { /* do nothing this is a service thing */ }
     }
 };
 //# sourceMappingURL=repl-normalize.js.map

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

@@ -93,8 +93,14 @@ exports.parseCommand = {
         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));
-        output.stdout(depthListToTextTree(toDepthMap(object), output.formatter));
+        if (parser.name === 'r-shell') {
+            const object = (0, format_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(result.parse.parsed));
+            output.stdout(depthListToTextTree(toDepthMap(object), output.formatter));
+        }
+        else {
+            // print the tree-sitter ast
+            output.stdout(JSON.stringify(result.parse.parsed, null, 2));
+        }
     }
 };
 //# sourceMappingURL=repl-parse.js.map

package/cli/repl/core.js

@@ -48,6 +48,7 @@ const scripts_info_1 = require("../common/scripts-info");
 const retriever_1 = require("../../r-bridge/retriever");
 const repl_main_1 = require("./commands/repl-main");
 const shell_1 = require("../../r-bridge/shell");
+const log_1 = require("../../util/log");
 let _replCompleterKeywords = undefined;
 function replCompleterKeywords() {
     if (_replCompleterKeywords === undefined) {
@@ -107,6 +108,9 @@ async function replProcessStatement(output, statement, parser, allowRSessionAcce
             }
             catch (e) {
                 output.stdout(`${bold(`Failed to execute command ${command}`)}: ${e?.message}. Using the ${bold('--verbose')} flag on startup may provide additional information.\n`);
+                if (log_1.log.settings.minLevel < 6 /* LogLevel.Fatal */) {
+                    console.error(e);
+                }
             }
         }
         else {

package/cli/repl/server/connection.js

@@ -152,7 +152,7 @@ class FlowRServerConnection {
     async sendFileAnalysisResponse(results, message) {
         let cfg = undefined;
         if (message.cfg) {
-            cfg = (0, cfg_1.extractCFG)(results.normalize);
+            cfg = (0, cfg_1.extractCFG)(results.normalize, results.dataflow?.graph);
         }
         const config = () => ({ context: message.filename ?? 'unknown', getId: (0, quads_1.defaultQuadIdGenerator)() });
         const sanitizedResults = sanitizeAnalysisResults(results);

package/cli/script-core/statistics-helper-core.js

@@ -59,7 +59,7 @@ async function getStatsForSingleFile(options) {
     if (stats.outputs.size === 1) {
         if (options['dump-json']) {
             const [, output] = [...stats.outputs.entries()][0];
-            const cfg = (0, cfg_1.extractCFG)(output.normalize);
+            const cfg = (0, cfg_1.extractCFG)(output.normalize, output.dataflow.graph);
             statistics_file_1.statisticsFileProvider.append('output-json', 'parse', await (0, print_1.printStepResult)(_00_parse_1.PARSE_WITH_R_SHELL_STEP, output.parse, 2 /* StepOutputFormat.Json */));
             statistics_file_1.statisticsFileProvider.append('output-json', 'normalize', await (0, print_1.printStepResult)(_10_normalize_1.NORMALIZE, output.normalize, 2 /* StepOutputFormat.Json */));
             statistics_file_1.statisticsFileProvider.append('output-json', 'dataflow', await (0, print_1.printStepResult)(_20_dataflow_1.STATIC_DATAFLOW, output.dataflow, 2 /* StepOutputFormat.Json */));

package/config.js

@@ -31,7 +31,6 @@ const defaultEngineConfigs = {
 };
 exports.defaultConfigOptions = {
     ignoreSourceCalls: false,
-    rPath: undefined,
     semantics: {
         environment: {
             overwriteBuiltIns: {
@@ -126,6 +125,14 @@ function getEngineConfig(engine) {
 }
 function loadConfigFromFile(configFile, workingDirectory) {
     if (configFile !== undefined) {
+        if (path_1.default.isAbsolute(configFile) && fs_1.default.existsSync(configFile)) {
+            log_1.log.trace(`Found config at ${configFile} (absolute)`);
+            const ret = parseConfig(fs_1.default.readFileSync(configFile, { encoding: 'utf-8' }));
+            if (ret) {
+                log_1.log.info(`Using config ${JSON.stringify(ret)}`);
+                return ret;
+            }
+        }
         let searchPath = path_1.default.resolve(workingDirectory);
         do {
             const configPath = path_1.default.join(searchPath, configFile);

package/dataflow/extractor.js

@@ -57,7 +57,7 @@ function resolveLinkToSideEffects(ast, graph) {
         if (typeof s !== 'object') {
             continue;
         }
-        cfg ??= (0, cfg_1.extractCFG)(ast).graph;
+        cfg ??= (0, cfg_1.extractCFG)(ast, graph).graph;
         /* this has to change whenever we add a new link to relations because we currently offer no abstraction for the type */
         const potentials = (0, identify_link_to_last_call_relation_1.identifyLinkToLastCallRelation)(s.id, cfg, graph, s.linkTo);
         for (const pot of potentials) {

package/dataflow/graph/dataflowgraph-builder.d.ts

@@ -85,57 +85,58 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
     /**
      * Adds a **read edge** (E1).
      *
-     * @param from - Vertex/NodeId
-     * @param to   - see from
+     * @param from - NodeId of the source vertex
+     * @param to   - Either a single or multiple target ids.
+     *               If you pass multiple this will construct a single edge for each of them.
      */
     reads(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**
      * Adds a **defined-by edge** (E2), with from as defined variable, and to
      * as a variable/function contributing to its definition.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     definedBy(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**
      * Adds a **call edge** (E5) with from as caller, and to as callee.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     calls(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**
      * Adds a **return edge** (E6) with from as function, and to as exit point.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     returns(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**
      * Adds a **defines-on-call edge** (E7) with from as variable, and to as its definition
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     definesOnCall(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**
      * Adds a **defined-by-on-call edge** with from as definition, and to as variable.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     definedByOnCall(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**
      * Adds an **argument edge** (E9) with from as function call, and to as argument.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     argument(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**
      * Adds a **non-standard evaluation edge** with from as vertex, and to as vertex.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     nse(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**
      * Adds a **side-effect-on-call edge** with from as vertex, and to as vertex.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     sideEffectOnCall(from: NodeId, to: DataflowGraphEdgeTarget): this;
     /**

package/dataflow/graph/dataflowgraph-builder.js

@@ -173,8 +173,9 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     /**
      * Adds a **read edge** (E1).
      *
-     * @param from - Vertex/NodeId
-     * @param to   - see from
+     * @param from - NodeId of the source vertex
+     * @param to   - Either a single or multiple target ids.
+     *               If you pass multiple this will construct a single edge for each of them.
      */
     reads(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.Reads);
@@ -183,7 +184,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
      * Adds a **defined-by edge** (E2), with from as defined variable, and to
      * as a variable/function contributing to its definition.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     definedBy(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.DefinedBy);
@@ -191,7 +192,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     /**
      * Adds a **call edge** (E5) with from as caller, and to as callee.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     calls(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.Calls);
@@ -199,7 +200,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     /**
      * Adds a **return edge** (E6) with from as function, and to as exit point.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     returns(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.Returns);
@@ -207,7 +208,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     /**
      * Adds a **defines-on-call edge** (E7) with from as variable, and to as its definition
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     definesOnCall(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.DefinesOnCall);
@@ -215,7 +216,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     /**
      * Adds a **defined-by-on-call edge** with from as definition, and to as variable.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     definedByOnCall(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.DefinedByOnCall);
@@ -223,7 +224,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     /**
      * Adds an **argument edge** (E9) with from as function call, and to as argument.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     argument(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.Argument);
@@ -231,7 +232,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     /**
      * Adds a **non-standard evaluation edge** with from as vertex, and to as vertex.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     nse(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.NonStandardEvaluation);
@@ -239,7 +240,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     /**
      * Adds a **side-effect-on-call edge** with from as vertex, and to as vertex.
      *
-     * @see reads for parameters.
+     * @see {@link DataflowGraphBuilder#reads|reads} for parameters.
      */
     sideEffectOnCall(from, to) {
         return this.edgeHelper(from, to, edge_1.EdgeType.SideEffectOnCall);

package/dataflow/graph/edge.d.ts

@@ -78,7 +78,7 @@ export declare const enum TraverseEdge {
  *
  * Counterpart of {@link edgeDoesNotIncludeType}.
  */
-export declare function edgeIncludesType(type: EdgeTypeBits, types: EdgeTypeBits): boolean;
+export declare function edgeIncludesType(type: EdgeTypeBits, typesToInclude: EdgeTypeBits): boolean;
 /**
  * Check if the given-edge type does not include the given type.
  * Counterpart of {@link edgeIncludesType}.

package/dataflow/graph/edge.js

@@ -85,8 +85,8 @@ function edgeTypesToNames(bits) {
  *
  * Counterpart of {@link edgeDoesNotIncludeType}.
  */
-function edgeIncludesType(type, types) {
-    return (types & type) !== 0;
+function edgeIncludesType(type, typesToInclude) {
+    return (typesToInclude & type) !== 0;
 }
 /**
  * Check if the given-edge type does not include the given type.

package/dataflow/graph/vertex.d.ts

@@ -21,7 +21,7 @@ export declare const ValidVertexTypeReverse: {
  */
 export interface ContainerLeafIndex {
     /**
-     * Destinctive lexeme of index e.g 'name' for `list(name = 'John')`
+     * Distinctive lexeme of index e.g. 'name' for `list(name = 'John')`
      */
     readonly lexeme: string;
     /**
@@ -201,21 +201,21 @@ export type DataflowGraphVertices<Vertex extends DataflowGraphVertexInfo = Dataf
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexValue|value vertex}.
  */
-export declare function isValueVertex(vertex: DataflowGraphVertexBase): vertex is DataflowGraphVertexValue;
+export declare function isValueVertex(vertex?: DataflowGraphVertexBase): vertex is DataflowGraphVertexValue;
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexUse|use vertex}.
  */
-export declare function isUseVertex(vertex: DataflowGraphVertexBase): vertex is DataflowGraphVertexUse;
+export declare function isUseVertex(vertex?: DataflowGraphVertexBase): vertex is DataflowGraphVertexUse;
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexFunctionCall|function call vertex}.
  */
-export declare function isFunctionCallVertex(vertex: DataflowGraphVertexBase): vertex is DataflowGraphVertexFunctionCall;
+export declare function isFunctionCallVertex(vertex?: DataflowGraphVertexBase): vertex is DataflowGraphVertexFunctionCall;
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexVariableDefinition|variable definition vertex}.
  */
-export declare function isVariableDefinitionVertex(vertex: DataflowGraphVertexBase): vertex is DataflowGraphVertexVariableDefinition;
+export declare function isVariableDefinitionVertex(vertex?: DataflowGraphVertexBase): vertex is DataflowGraphVertexVariableDefinition;
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexFunctionDefinition|function definition vertex}.
  */
-export declare function isFunctionDefinitionVertex(vertex: DataflowGraphVertexBase): vertex is DataflowGraphVertexFunctionDefinition;
+export declare function isFunctionDefinitionVertex(vertex?: DataflowGraphVertexBase): vertex is DataflowGraphVertexFunctionDefinition;
 export {};

package/dataflow/graph/vertex.js

@@ -24,30 +24,30 @@ function isParentContainerIndex(index) {
  * Check if the given vertex is a {@link DataflowGraphVertexValue|value vertex}.
  */
 function isValueVertex(vertex) {
-    return vertex.tag === VertexType.Value;
+    return vertex?.tag === VertexType.Value;
 }
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexUse|use vertex}.
  */
 function isUseVertex(vertex) {
-    return vertex.tag === VertexType.Use;
+    return vertex?.tag === VertexType.Use;
 }
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexFunctionCall|function call vertex}.
  */
 function isFunctionCallVertex(vertex) {
-    return vertex.tag === VertexType.FunctionCall;
+    return vertex?.tag === VertexType.FunctionCall;
 }
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexVariableDefinition|variable definition vertex}.
  */
 function isVariableDefinitionVertex(vertex) {
-    return vertex.tag === VertexType.VariableDefinition;
+    return vertex?.tag === VertexType.VariableDefinition;
 }
 /**
  * Check if the given vertex is a {@link DataflowGraphVertexFunctionDefinition|function definition vertex}.
  */
 function isFunctionDefinitionVertex(vertex) {
-    return vertex.tag === VertexType.FunctionDefinition;
+    return vertex?.tag === VertexType.FunctionDefinition;
 }
 //# sourceMappingURL=vertex.js.map

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

@@ -1,7 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.processAccess = processAccess;
-const assert_1 = require("../../../../../../util/assert");
 const known_call_handling_1 = require("../known-call-handling");
 const r_function_call_1 = require("../../../../../../r-bridge/lang-4.x/ast/model/nodes/r-function-call");
 const logger_1 = require("../../../../../logger");
@@ -35,9 +34,12 @@ function processAccess(name, args, rootId, data, config) {
         return (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data, forceArgs: config.forceArgs }).information;
     }
     const head = args[0];
-    (0, assert_1.guard)(head !== r_function_call_1.EmptyArgument, () => `Access ${name.content} has no source, impossible!`);
     let fnCall;
-    if (!config.treatIndicesAsString) {
+    if (head === r_function_call_1.EmptyArgument) {
+        // in this case we may be within a pipe
+        fnCall = (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data, forceArgs: config.forceArgs });
+    }
+    else if (!config.treatIndicesAsString) {
         /* within an access operation which treats its fields, we redefine the table assignment ':=' as a trigger if this is to be treated as a definition */
         // do we have a local definition that needs to be recovered?
         fnCall = processNumberBasedAccess(data, name, args, rootId, config, head);
@@ -46,7 +48,9 @@ function processAccess(name, args, rootId, data, config) {
         fnCall = processStringBasedAccess(args, data, name, rootId, config);
     }
     const info = fnCall.information;
-    info.graph.addEdge(name.info.id, fnCall.processedArguments[0]?.entryPoint ?? head.info.id, edge_1.EdgeType.Returns);
+    if (head !== r_function_call_1.EmptyArgument) {
+        info.graph.addEdge(name.info.id, fnCall.processedArguments[0]?.entryPoint ?? head.info.id, edge_1.EdgeType.Returns);
+    }
     /* access always reads all of its indices */
     for (const arg of fnCall.processedArguments) {
         if (arg !== undefined) {
@@ -70,7 +74,7 @@ function processAccess(name, args, rootId, data, config) {
         unknownReferences: (0, environment_1.makeAllMaybe)(info.unknownReferences, info.graph, info.environment, false),
         entryPoint: rootId,
         /** it is, to be precise, the accessed element we want to map to maybe */
-        in: info.in.map(ref => {
+        in: head === r_function_call_1.EmptyArgument ? info.in : info.in.map(ref => {
             if (ref.nodeId === head.value?.info.id) {
                 return (0, environment_1.makeReferenceMaybe)(ref, info.graph, info.environment, false);
             }

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

@@ -83,10 +83,10 @@ function sourceRequest(rootId, request, data, information, getId) {
     }
     // take the entry point as well as all the written references, and give them a control dependency to the source call to show that they are conditional
     if (dataflow.graph.hasVertex(dataflow.entryPoint)) {
-        dataflow.graph.addControlDependency(dataflow.entryPoint, rootId);
+        dataflow.graph.addControlDependency(dataflow.entryPoint, rootId, true);
     }
     for (const out of dataflow.out) {
-        dataflow.graph.addControlDependency(out.nodeId, rootId);
+        dataflow.graph.addControlDependency(out.nodeId, rootId, true);
     }
     // update our graph with the sourced file's information
     const newInformation = { ...information };

package/documentation/doc-util/doc-cfg.js

@@ -6,12 +6,12 @@ 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");
 async function getCfg(shell, code) {
-    const steps = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_NORMALIZE_PIPELINE, {
+    const steps = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
         parser: shell,
         request: (0, retriever_1.requestFromInput)(code)
     }).allRemainingSteps();
     return {
-        info: (0, cfg_1.extractCFG)(steps.normalize),
+        info: (0, cfg_1.extractCFG)(steps.normalize, steps.dataflow?.graph),
         ast: steps.normalize
     };
 }

package/documentation/doc-util/doc-types.js

@@ -312,9 +312,9 @@ function implSnippet(node, program, showName = true, nesting = 0) {
     const sep = node.comments ? '  \n' : '\n';
     let text = node.comments?.join('\n') ?? '';
     const code = node.node.getFullText(program.getSourceFile(node.node.getSourceFile().fileName));
-    text += `\n<details><summary style="color:gray">Defined at <a href="${getTypePathLink(node)}">${getTypePathLink(node, '.')}</a></summary>\n\n${(0, doc_code_1.codeBlock)('ts', code)}\n\n</details>\n`;
-    const init = showName ? ` * ${bold}[${node.name}](${getTypePathLink(node)})${bold} ${sep}${indent}` : '';
-    return ` ${indent} ${showName ? init : ''} ${text.replaceAll('\t', '    ').split(/\n/g).join(`\n${indent}   `)}`;
+    text += `\n${indent}<details><summary style="color:gray">Defined at <a href="${getTypePathLink(node)}">${getTypePathLink(node, '.')}</a></summary>\n\n${(0, doc_code_1.codeBlock)('ts', code)}\n\n</details>\n`;
+    const init = showName ? `* ${bold}[${node.name}](${getTypePathLink(node)})${bold} ${sep}${indent}` : '';
+    return ` ${indent}${showName ? init : ''} ${text.replaceAll('\t', '    ').split(/\n/g).join(`\n${indent}   `)}`;
 }
 exports.mermaidHide = ['Leaf', 'Location', 'Namespace', 'Base', 'WithChildren', 'Partial', 'RAccessBase'];
 function printHierarchy({ program, hierarchy, root, collapseFromNesting = 1, initialNesting = 0, maxDepth = 20 }) {

package/documentation/print-interface-wiki.js

@@ -175,7 +175,6 @@ ${(0, doc_code_1.codeBlock)('shell', ':query @config')}
 The following summarizes the configuration options:
 
 - \`ignoreSourceCalls\`: If set to \`true\`, _flowR_ will ignore source calls when analyzing the code, i.e., ignoring the inclusion of other files.
-- \`rPath\`: The path to the R executable. If not set, _flowR_ will try to find the R executable in the system's PATH.
 - \`semantics\`: allows to configure the way _flowR_ handles R, although we currently only support \`semantics/environment/overwriteBuiltIns\`. 
   You may use this to overwrite _flowR_'s handling of built-in function and even completely clear the preset definitions shipped with flowR. 
   See [Configure BuiltIn Semantics](#configure-builtin-semantics) for more information.
@@ -191,7 +190,6 @@ So you can configure _flowR_ by adding a file like the following:
 
 ${(0, doc_code_1.codeBlock)('json', JSON.stringify({
         ignoreSourceCalls: true,
-        rPath: '/usr/bin/R',
         semantics: {
             environment: {
                 overwriteBuiltIns: {