@eagleoutice/flowr 2.2.12 → 2.2.14

package/linter/rules/2-file-path-validity.d.ts

@@ -0,0 +1,48 @@
+import type { LintingResult } from '../linter-format';
+import type { MergeableRecord } from '../../util/objects';
+import type { SourceRange } from '../../util/range';
+import type { ParentInformation } from '../../r-bridge/lang-4.x/ast/model/processing/decorate';
+import type { FlowrSearchElementFromQuery } from '../../search/flowr-search';
+import type { FunctionInfo } from '../../queries/catalog/dependencies-query/function-info/function-info';
+export interface FilePathValidityResult extends LintingResult {
+    filePath: string;
+    range: SourceRange;
+}
+export interface FilePathValidityConfig extends MergeableRecord {
+    /**
+     * The set of functions that should additionally be considered as reading a file path.
+     * Entries in this array use the {@link FunctionInfo} format from the dependencies query.
+     */
+    additionalReadFunctions: FunctionInfo[];
+    /**
+     * The set of functions that should additionally be considered as writing to a file path.
+     * Entries in this array use the {@link FunctionInfo} format from the dependencies query.
+     */
+    additionalWriteFunctions: FunctionInfo[];
+    /**
+     * Whether unknown file paths should be included as linting results.
+     */
+    includeUnknown: boolean;
+}
+export interface FilePathValidityMetadata extends MergeableRecord {
+    totalReads: number;
+    totalUnknown: number;
+    totalWritesBeforeAlways: number;
+    totalValid: number;
+}
+export declare const R2_FILE_PATH_VALIDITY: {
+    readonly createSearch: (config: FilePathValidityConfig) => import("../../search/flowr-search-builder").FlowrSearchBuilder<"from-query", [], ParentInformation, import("../../search/flowr-search").FlowrSearchElements<ParentInformation, FlowrSearchElementFromQuery<ParentInformation>[]>>;
+    readonly processSearchResult: (elements: import("../../search/flowr-search").FlowrSearchElements<ParentInformation, FlowrSearchElementFromQuery<ParentInformation>[]>, config: FilePathValidityConfig, data: {
+        normalize: import("../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+        dataflow: import("../../dataflow/info").DataflowInformation;
+    }) => {
+        results: FilePathValidityResult[];
+        ".meta": FilePathValidityMetadata;
+    };
+    readonly prettyPrint: (result: FilePathValidityResult) => string;
+    readonly defaultConfig: {
+        readonly additionalReadFunctions: [];
+        readonly additionalWriteFunctions: [];
+        readonly includeUnknown: false;
+    };
+};

package/linter/rules/2-file-path-validity.js

@@ -0,0 +1,93 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.R2_FILE_PATH_VALIDITY = void 0;
+const linter_format_1 = require("../linter-format");
+const flowr_search_builder_1 = require("../../search/flowr-search-builder");
+const dfg_1 = require("../../util/mermaid/dfg");
+const dependencies_query_format_1 = require("../../queries/catalog/dependencies-query/dependencies-query-format");
+const built_in_source_1 = require("../../dataflow/internal/process/functions/call/built-in/built-in-source");
+const logic_1 = require("../../util/logic");
+const config_1 = require("../../config");
+const retriever_1 = require("../../r-bridge/retriever");
+const read_functions_1 = require("../../queries/catalog/dependencies-query/function-info/read-functions");
+const write_functions_1 = require("../../queries/catalog/dependencies-query/function-info/write-functions");
+const extract_cfg_1 = require("../../control-flow/extract-cfg");
+const happens_before_1 = require("../../control-flow/happens-before");
+exports.R2_FILE_PATH_VALIDITY = {
+    createSearch: (config) => flowr_search_builder_1.Q.fromQuery({
+        type: 'dependencies',
+        // we only want to check read and write functions, so we explicitly clear all others
+        ignoreDefaultFunctions: true,
+        readFunctions: read_functions_1.ReadFunctions.concat(config.additionalReadFunctions),
+        writeFunctions: write_functions_1.WriteFunctions.concat(config.additionalWriteFunctions)
+    }),
+    processSearchResult: (elements, config, data) => {
+        const cfg = (0, extract_cfg_1.extractSimpleCfg)(data.normalize).graph;
+        const metadata = {
+            totalReads: 0,
+            totalUnknown: 0,
+            totalWritesBeforeAlways: 0,
+            totalValid: 0
+        };
+        return {
+            results: elements.getElements().flatMap(element => {
+                const results = element.queryResult;
+                const matchingRead = results.readData.find(r => r.nodeId == element.node.info.id);
+                if (!matchingRead) {
+                    return [];
+                }
+                metadata.totalReads++;
+                const range = element.node.info.fullRange;
+                // check if we can't parse the file path statically
+                if (matchingRead.source === dependencies_query_format_1.Unknown) {
+                    metadata.totalUnknown++;
+                    if (config.includeUnknown) {
+                        return [{
+                                range,
+                                filePath: dependencies_query_format_1.Unknown,
+                                certainty: linter_format_1.LintingCertainty.Maybe
+                            }];
+                    }
+                    else {
+                        return [];
+                    }
+                }
+                // check if any write to the same file happens before the read, and exclude this case if so
+                const writesToFile = results.writtenData.filter(r => samePath(r.destination, matchingRead.source));
+                const writesBefore = writesToFile.map(w => (0, happens_before_1.happensBefore)(cfg, w.nodeId, element.node.info.id));
+                if (writesBefore.some(w => w === logic_1.Ternary.Always)) {
+                    metadata.totalWritesBeforeAlways++;
+                    return [];
+                }
+                // check if the file exists!
+                const paths = (0, built_in_source_1.findSource)(matchingRead.source, {
+                    referenceChain: element.node.info.file ? [(0, retriever_1.requestFromInput)(`file://${element.node.info.file}`)] : []
+                });
+                if (paths && paths.length) {
+                    metadata.totalValid++;
+                    return [];
+                }
+                return [{
+                        range,
+                        filePath: matchingRead.source,
+                        certainty: writesBefore && writesBefore.length && writesBefore.every(w => w === logic_1.Ternary.Maybe) ? linter_format_1.LintingCertainty.Maybe : linter_format_1.LintingCertainty.Definitely
+                    }];
+            }),
+            '.meta': metadata
+        };
+    },
+    prettyPrint: result => `Path ${result.filePath} at ${(0, dfg_1.formatRange)(result.range)}`,
+    defaultConfig: {
+        additionalReadFunctions: [],
+        additionalWriteFunctions: [],
+        includeUnknown: false
+    }
+};
+function samePath(a, b) {
+    if ((0, config_1.getConfig)().solver.resolveSource?.ignoreCapitalization === true) {
+        a = a.toLowerCase();
+        b = b.toLowerCase();
+    }
+    return a === b;
+}
+//# sourceMappingURL=2-file-path-validity.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.2.12",
+  "version": "2.2.14",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {
@@ -12,6 +12,7 @@
     "url": "https://github.com/flowr-analysis/flowr/issues"
   },
   "scripts": {
+    "setup:dev": "git lfs fetch && npm ci && git config --local core.hooksPath .githooks/ && git push --dry-run",
     "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",
@@ -33,13 +34,15 @@
     "wiki:search-api": "ts-node src/documentation/print-search-wiki.ts",
     "wiki:linting-and-testing": "ts-node src/documentation/print-linting-and-testing-wiki.ts",
     "wiki:interface": "ts-node src/documentation/print-interface-wiki.ts",
+    "wiki:onboarding": "ts-node src/documentation/print-onboarding-wiki.ts",
+    "wiki:faq": "ts-node src/documentation/print-faq-wiki.ts",
     "wiki:cfg": "ts-node src/documentation/print-cfg-wiki.ts",
+    "wiki:linter": "ts-node src/documentation/print-linter-wiki.ts",
     "gen:readme": "ts-node src/documentation/print-readme.ts",
     "build": "tsc --project .",
     "build-dev": "npm run build && npm run build:copy-wasm",
-    "build:bundle-flowr": "npm run build && esbuild --bundle dist/src/cli/flowr.js --platform=node --tree-shaking=true --bundle --minify --external:clipboardy --target=node22 --outfile=dist/src/cli/flowr.min.js && npm run build:copy-wasm-min",
-    "build:copy-wasm": "mkdir -p dist/src/r-bridge/lang-4.x/tree-sitter/ && cp src/r-bridge/lang-4.x/tree-sitter/tree-sitter-r.wasm src/r-bridge/lang-4.x/tree-sitter/tree-sitter.wasm dist/src/r-bridge/lang-4.x/tree-sitter/",
-    "build:copy-wasm-min": "mkdir -p dist/src/cli && cp src/r-bridge/lang-4.x/tree-sitter/tree-sitter-r.wasm src/r-bridge/lang-4.x/tree-sitter/tree-sitter.wasm dist/src/cli",
+    "build:bundle-flowr": "npm run build && esbuild --bundle dist/src/cli/flowr.js --platform=node --tree-shaking=true --bundle --minify --external:clipboardy --target=node22 --outfile=dist/src/cli/flowr.min.js && npm run build:copy-wasm",
+    "build:copy-wasm": "mkdir -p dist/node_modules/@eagleoutice/tree-sitter-r/ && mkdir -p dist/node_modules/web-tree-sitter && cp node_modules/@eagleoutice/tree-sitter-r/tree-sitter-r.wasm dist/node_modules/@eagleoutice/tree-sitter-r/  && cp node_modules/web-tree-sitter/tree-sitter.wasm dist/node_modules/web-tree-sitter/",
     "lint-local": "npx eslint --version && npx eslint src/ test/ --rule \"no-warning-comments: off\"",
     "lint": "npm run license-compat -- --summary && npx eslint --version && npx eslint src/ test/",
     "license-compat": "license-checker --onlyAllow 'MIT;MIT OR X11;GPLv2;LGPL;GNUGPL;ISC;Apache-2.0;FreeBSD;BSD-2-Clause;clearbsd;ModifiedBSD;BSD-3-Clause;Python-2.0;Unlicense;WTFPL;BlueOak-1.0.0;CC-BY-4.0;CC-BY-3.0;CC0-1.0;0BSD'",
@@ -175,7 +178,7 @@
     "@eagleoutice/eslint-config-flowr": "^1.0.17",
     "@eslint/eslintrc": "^3.2.0",
     "@eslint/js": "^9.20.0",
-    "@j-ulrich/release-it-regex-bumper": "^5.2.0",
+    "@j-ulrich/release-it-regex-bumper": "^5.3.0",
     "@types/command-line-args": "^5.2.3",
     "@types/command-line-usage": "^5.0.4",
     "@types/n-readlines": "^1.0.6",
@@ -190,7 +193,7 @@
     "eslint": "^9.20.1",
     "license-checker": "^25.0.1",
     "npm-run-all": "^4.1.5",
-    "release-it": "^18.1.2",
+    "release-it": "^19.0.2",
     "ts-node": "^10.9.2",
     "typedoc": "^0.27.7",
     "typedoc-plugin-missing-exports": "^3.1.0",
@@ -200,6 +203,7 @@
     "vitest": "^3.0.6"
   },
   "dependencies": {
+    "@eagleoutice/tree-sitter-r": "^1.1.2",
     "@xmldom/xmldom": "^0.9.7",
     "clipboardy": "^4.0.0",
     "command-line-args": "^6.0.1",

package/queries/catalog/call-context-query/call-context-query-executor.js

@@ -4,7 +4,7 @@ exports.executeCallContextQueries = executeCallContextQueries;
 const node_id_1 = require("../../../r-bridge/lang-4.x/ast/model/processing/node-id");
 const vertex_1 = require("../../../dataflow/graph/vertex");
 const edge_1 = require("../../../dataflow/graph/edge");
-const cfg_1 = require("../../../util/cfg/cfg");
+const extract_cfg_1 = require("../../../control-flow/extract-cfg");
 const two_layer_collector_1 = require("../../two-layer-collector");
 const objects_1 = require("../../../util/objects");
 const identify_link_to_last_call_relation_1 = require("./identify-link-to-last-call-relation");
@@ -85,7 +85,7 @@ function retrieveAllCallAliases(nodeId, graph) {
     const aliases = new Map();
     const visited = new Set();
     /* we store the current call name */
-    const queue = [[(0, node_id_1.recoverContent)(nodeId, graph) ?? '', nodeId]];
+    let queue = [[(0, node_id_1.recoverContent)(nodeId, graph) ?? '', nodeId]];
     while (queue.length > 0) {
         const [str, id] = queue.shift();
         if (visited.has(id)) {
@@ -111,7 +111,7 @@ function retrieveAllCallAliases(nodeId, graph) {
                 .filter(([, { types }]) => (0, edge_1.edgeIncludesType)(types, edge_1.EdgeType.Reads | edge_1.EdgeType.DefinedBy | edge_1.EdgeType.DefinedByOnCall))
                 .map(([t]) => [(0, node_id_1.recoverContent)(t, graph) ?? '', t]);
             /** only follow defined-by and reads */
-            queue.push(...x);
+            queue = queue.concat(x);
             continue;
         }
         let track = edge_1.EdgeType.Calls | edge_1.EdgeType.Reads | edge_1.EdgeType.DefinedBy | edge_1.EdgeType.DefinedByOnCall;
@@ -180,7 +180,7 @@ function executeCallContextQueries({ dataflow: { graph }, ast }, queries) {
     const { promotedQueries, requiresCfg } = promoteQueryCallNames(queries);
     let cfg = undefined;
     if (requiresCfg) {
-        cfg = (0, cfg_1.extractCFG)(ast, graph);
+        cfg = (0, extract_cfg_1.extractCfg)(ast, graph, []);
     }
     const queriesWhichWantAliases = promotedQueries.filter(q => q.includeAliases);
     for (const [nodeId, info] of graph.vertices(true)) {
@@ -203,7 +203,7 @@ function executeCallContextQueries({ dataflow: { graph }, ast }, queries) {
                 }
             }
         }
-        for (const query of promotedQueries.filter(q => q.callName.test(info.name))) {
+        for (const query of promotedQueries.filter(q => !q.includeAliases && q.callName.test(info.name))) {
             const file = ast.idMap.get(nodeId)?.info.file;
             if (!doesFilepathMatch(file, query.fileFilter)) {
                 continue;

package/queries/catalog/call-context-query/call-context-query-format.d.ts

@@ -1,7 +1,7 @@
 import type { BaseQueryFormat, BaseQueryResult } from '../../base-query-format';
 import type { NodeId } from '../../../r-bridge/lang-4.x/ast/model/processing/node-id';
 import { executeCallContextQueries } from './call-context-query-executor';
-import type { OutputFormatter } from '../../../util/ansi';
+import type { OutputFormatter } from '../../../util/text/ansi';
 import Joi from 'joi';
 import type { PipelineOutput } from '../../../core/steps/pipeline/pipeline';
 import type { DEFAULT_DATAFLOW_PIPELINE } from '../../../core/steps/pipeline/default-pipelines';
@@ -56,7 +56,7 @@ export interface DefaultCallContextQueryFormat<RegexType extends RegExp | string
  * For now, this uses the static Control-Flow-Graph produced by flowR as the FD over-approximation is still not stable (see #1005).
  * In short, this means that we are unable to detect origins over function call boundaries but plan on being more precise in the future.
  */
-interface LinkToLastCall<CallName extends RegExp | string = RegExp | string> extends BaseQueryFormat {
+export interface LinkToLastCall<CallName extends RegExp | string = RegExp | string> extends BaseQueryFormat {
     readonly type: 'link-to-last-call';
     /** Regex regarding the function name of the last call. Similar to {@link DefaultCallContextQueryFormat#callName}, strings are interpreted as a `RegExp`. */
     readonly callName: CallName;
@@ -110,5 +110,5 @@ export declare const CallContextQueryDefinition: {
     readonly executor: typeof executeCallContextQueries;
     readonly asciiSummarizer: (formatter: OutputFormatter, processed: PipelineOutput<typeof DEFAULT_DATAFLOW_PIPELINE>, queryResults: BaseQueryResult, result: string[]) => boolean;
     readonly schema: Joi.ObjectSchema<any>;
+    readonly flattenInvolvedNodes: (queryResults: BaseQueryResult) => NodeId[];
 };
-export {};

package/queries/catalog/call-context-query/call-context-query-format.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.CallContextQueryDefinition = void 0;
 const call_context_query_executor_1 = require("./call-context-query-executor");
-const ansi_1 = require("../../../util/ansi");
-const time_1 = require("../../../util/time");
+const ansi_1 = require("../../../util/text/ansi");
+const time_1 = require("../../../util/text/time");
 const joi_1 = __importDefault(require("joi"));
 const query_print_1 = require("../../query-print");
 const identify_link_to_last_call_relation_1 = require("./identify-link-to-last-call-relation");
@@ -39,6 +39,10 @@ exports.CallContextQueryDefinition = {
             includeUndefinedFiles: joi_1.default.boolean().optional().description('If `fileFilter` is set, but a nodes `file` attribute is `undefined`, should we include it in the results? Defaults to `true`.')
         }).optional().description('Filter that, when set, a node\'s file attribute must match to be considered'),
         linkTo: joi_1.default.alternatives(CallContextQueryLinkTo, joi_1.default.array().items(CallContextQueryLinkTo)).optional().description('Links the current call to the last call of the given kind. This way, you can link a call like `points` to the latest graphics plot etc.')
-    }).description('Call context query used to find calls in the dataflow graph')
+    }).description('Call context query used to find calls in the dataflow graph'),
+    flattenInvolvedNodes: (queryResults) => {
+        const out = queryResults;
+        return Object.values(out.kinds).flatMap(({ subkinds }) => Object.values(subkinds).flatMap(subkinds => subkinds.map(subkind => subkind.id)));
+    }
 };
 //# sourceMappingURL=call-context-query-format.js.map

package/queries/catalog/call-context-query/identify-link-to-last-call-relation.d.ts

@@ -1,12 +1,12 @@
 import type { NodeId } from '../../../r-bridge/lang-4.x/ast/model/processing/node-id';
-import type { ControlFlowGraph } from '../../../util/cfg/cfg';
 import type { DataflowGraph } from '../../../dataflow/graph/graph';
 import type { DataflowGraphVertexFunctionCall } from '../../../dataflow/graph/vertex';
 import { RType } from '../../../r-bridge/lang-4.x/ast/model/type';
 import type { RNodeWithParent } from '../../../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { LinkTo } from './call-context-query-format';
+import type { ControlFlowGraph } from '../../../control-flow/control-flow-graph';
 export declare enum CallTargets {
-    /** call targets a function that is not defined locally (e.g., the call targets a library function) */
+    /** call targets a function that is not defined locally in the script (e.g., the call targets a library function) */
     OnlyGlobal = "global",
     /** call targets a function that is defined locally or globally, but must include a global function */
     MustIncludeGlobal = "must-include-global",

package/queries/catalog/call-context-query/identify-link-to-last-call-relation.js

@@ -5,7 +5,7 @@ exports.satisfiesCallTargets = satisfiesCallTargets;
 exports.getValueOfArgument = getValueOfArgument;
 exports.identifyLinkToLastCallRelation = identifyLinkToLastCallRelation;
 const graph_1 = require("../../../dataflow/graph/graph");
-const visitor_1 = require("../../../util/cfg/visitor");
+const simple_visitor_1 = require("../../../control-flow/simple-visitor");
 const vertex_1 = require("../../../dataflow/graph/vertex");
 const edge_1 = require("../../../dataflow/graph/edge");
 const resolve_by_name_1 = require("../../../dataflow/environments/resolve-by-name");
@@ -17,7 +17,7 @@ const r_function_call_1 = require("../../../r-bridge/lang-4.x/ast/model/nodes/r-
 const cascade_action_1 = require("./cascade-action");
 var CallTargets;
 (function (CallTargets) {
-    /** call targets a function that is not defined locally (e.g., the call targets a library function) */
+    /** call targets a function that is not defined locally in the script (e.g., the call targets a library function) */
     CallTargets["OnlyGlobal"] = "global";
     /** call targets a function that is defined locally or globally, but must include a global function */
     CallTargets["MustIncludeGlobal"] = "must-include-global";
@@ -29,16 +29,19 @@ var CallTargets;
     CallTargets["Any"] = "any";
 })(CallTargets || (exports.CallTargets = CallTargets = {}));
 function satisfiesCallTargets(id, graph, callTarget) {
-    const callVertex = graph.get(id);
-    if (callVertex === undefined || callVertex[0].tag !== vertex_1.VertexType.FunctionCall) {
+    const callVertex = graph.getVertex(id, true);
+    if (callVertex === undefined || callVertex.tag !== vertex_1.VertexType.FunctionCall) {
+        return 'no';
+    }
+    const outgoing = graph.outgoingEdges(id);
+    if (outgoing === undefined) {
         return 'no';
     }
-    const [info, outgoing] = callVertex;
     const callTargets = [...outgoing]
-        .filter(([, e]) => (0, edge_1.edgeIncludesType)(e.types, edge_1.EdgeType.Calls))
+        .filter(([, { types }]) => (0, edge_1.edgeIncludesType)(types, edge_1.EdgeType.Calls))
         .map(([t]) => t);
     let builtIn = false;
-    if (info.environment === undefined) {
+    if (callVertex.environment === undefined) {
         /* if we have a call with an unbound environment,
          * this only happens if we are sure of built-in relations and want to save references
          */
@@ -49,8 +52,8 @@ function satisfiesCallTargets(id, graph, callTarget) {
          * for performance and scoping reasons, flowR will not identify the global linkage,
          * including any potential built-in mapping.
          */
-        const reResolved = (0, resolve_by_name_1.resolveByName)(info.name, info.environment, identifier_1.ReferenceType.Unknown);
-        if (reResolved?.some(t => t.definedAt === built_in_1.BuiltIn)) {
+        const reResolved = (0, resolve_by_name_1.resolveByName)(callVertex.name, callVertex.environment, identifier_1.ReferenceType.Unknown);
+        if (reResolved?.some(t => (0, built_in_1.isBuiltIn)(t.definedAt))) {
             builtIn = true;
         }
     }
@@ -58,19 +61,19 @@ function satisfiesCallTargets(id, graph, callTarget) {
         case CallTargets.Any:
             return callTargets;
         case CallTargets.OnlyGlobal:
-            if (callTargets.length === 0) {
-                return builtIn ? [built_in_1.BuiltIn] : [];
+            if (callTargets.every(built_in_1.isBuiltIn)) {
+                return builtIn ? ['built-in'] : [];
             }
             else {
                 return 'no';
             }
         case CallTargets.MustIncludeGlobal:
-            return builtIn || callTargets.length === 0 ? [...callTargets, built_in_1.BuiltIn] : 'no';
+            return builtIn || callTargets.length === 0 ? [...callTargets, 'built-in'] : 'no';
         case CallTargets.OnlyLocal:
             return !builtIn && callTargets.length > 0 ? callTargets : 'no';
         case CallTargets.MustIncludeLocal:
             if (callTargets.length > 0) {
-                return builtIn ? [...callTargets, built_in_1.BuiltIn] : callTargets;
+                return builtIn ? [...callTargets, 'built-in'] : callTargets;
             }
             else {
                 return 'no';
@@ -105,25 +108,25 @@ function getValueOfArgument(graph, call, argument, additionalAllowedTypes) {
     }
 }
 function identifyLinkToLastCallRelation(from, cfg, graph, { callName, ignoreIf, cascadeIf }) {
-    const found = [];
     if (ignoreIf && ignoreIf(from, graph)) {
-        return found;
+        return [];
     }
-    (0, visitor_1.visitCfgInReverseOrder)(cfg, from, node => {
+    const found = [];
+    (0, simple_visitor_1.visitCfgInReverseOrder)(cfg, [from], node => {
         /* we ignore the start id as it cannot be the last call */
         if (node === from) {
             return;
         }
-        const vertex = graph.get(node);
-        if (vertex === undefined || vertex[0].tag !== vertex_1.VertexType.FunctionCall) {
+        const vertex = graph.getVertex(node, true);
+        if (vertex === undefined || vertex.tag !== vertex_1.VertexType.FunctionCall) {
             return;
         }
-        if (callName.test(vertex[0].name)) {
-            const act = cascadeIf ? cascadeIf(vertex[0], from, graph) : cascade_action_1.CascadeAction.Stop;
+        if (callName.test(vertex.name)) {
+            const act = cascadeIf ? cascadeIf(vertex, from, graph) : cascade_action_1.CascadeAction.Stop;
             if (act === cascade_action_1.CascadeAction.Skip) {
                 return;
             }
-            const tar = satisfiesCallTargets(vertex[0].id, graph, CallTargets.MustIncludeGlobal);
+            const tar = satisfiesCallTargets(vertex.id, graph, CallTargets.MustIncludeGlobal);
             if (tar === 'no') {
                 return act === cascade_action_1.CascadeAction.Stop;
             }

package/queries/catalog/cluster-query/cluster-query-format.d.ts

@@ -2,6 +2,7 @@ import type { BaseQueryFormat, BaseQueryResult } from '../../base-query-format';
 import Joi from 'joi';
 import type { DataflowGraphClusters } from '../../../dataflow/cluster';
 import { executeDataflowClusterQuery } from './cluster-query-executor';
+import type { NodeId } from '../../../r-bridge/lang-4.x/ast/model/processing/node-id';
 /**
  * Calculates and returns all clusters encountered in the dataflow graph.
  */
@@ -14,7 +15,7 @@ export interface DataflowClusterQueryResult extends BaseQueryResult {
 }
 export declare const ClusterQueryDefinition: {
     readonly executor: typeof executeDataflowClusterQuery;
-    readonly asciiSummarizer: (formatter: import("../../../util/ansi").OutputFormatter, processed: import("../../../core/steps/pipeline/pipeline").PipelineOutput<import("../../../core/steps/pipeline/pipeline").Pipeline<{
+    readonly asciiSummarizer: (formatter: import("../../../util/text/ansi").OutputFormatter, processed: import("../../../core/steps/pipeline/pipeline").PipelineOutput<import("../../../core/steps/pipeline/pipeline").Pipeline<{
         readonly name: "parse";
         readonly humanReadableName: "parse with R shell";
         readonly description: "Parse the given R code into an AST";
@@ -69,4 +70,5 @@ export declare const ClusterQueryDefinition: {
         readonly dependencies: readonly ["normalize"];
     }>>, queryResults: BaseQueryResult, result: string[]) => true;
     readonly schema: Joi.ObjectSchema<any>;
+    readonly flattenInvolvedNodes: (queryResults: BaseQueryResult) => NodeId[];
 };

package/queries/catalog/cluster-query/cluster-query-format.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ClusterQueryDefinition = void 0;
-const ansi_1 = require("../../../util/ansi");
+const ansi_1 = require("../../../util/text/ansi");
 const joi_1 = __importDefault(require("joi"));
 const cluster_query_executor_1 = require("./cluster-query-executor");
 const dfg_1 = require("../../../util/mermaid/dfg");
@@ -27,6 +27,10 @@ exports.ClusterQueryDefinition = {
     },
     schema: joi_1.default.object({
         type: joi_1.default.string().valid('dataflow-cluster').required().description('The type of the query.'),
-    }).description('The cluster query calculates and returns all clusters in the dataflow graph.')
+    }).description('The cluster query calculates and returns all clusters in the dataflow graph.'),
+    flattenInvolvedNodes: (queryResults) => {
+        const out = queryResults;
+        return out.clusters.flatMap(({ members }) => members);
+    }
 };
 //# sourceMappingURL=cluster-query-format.js.map

package/queries/catalog/config-query/config-query-format.d.ts

@@ -1,6 +1,6 @@
 import type { BaseQueryFormat, BaseQueryResult } from '../../base-query-format';
 import { executeConfigQuery } from './config-query-executor';
-import { type OutputFormatter } from '../../../util/ansi';
+import { type OutputFormatter } from '../../../util/text/ansi';
 import Joi from 'joi';
 import type { FlowrConfigOptions } from '../../../config';
 export interface ConfigQuery extends BaseQueryFormat {
@@ -13,4 +13,5 @@ export declare const ConfigQueryDefinition: {
     readonly executor: typeof executeConfigQuery;
     readonly asciiSummarizer: (formatter: OutputFormatter, _processed: unknown, queryResults: BaseQueryResult, result: string[]) => boolean;
     readonly schema: Joi.ObjectSchema<any>;
+    readonly flattenInvolvedNodes: () => never[];
 };

package/queries/catalog/config-query/config-query-format.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ConfigQueryDefinition = void 0;
 const config_query_executor_1 = require("./config-query-executor");
-const ansi_1 = require("../../../util/ansi");
-const time_1 = require("../../../util/time");
+const ansi_1 = require("../../../util/text/ansi");
+const time_1 = require("../../../util/text/time");
 const joi_1 = __importDefault(require("joi"));
 const json_1 = require("../../../util/json");
 exports.ConfigQueryDefinition = {
@@ -19,6 +19,7 @@ exports.ConfigQueryDefinition = {
     },
     schema: joi_1.default.object({
         type: joi_1.default.string().valid('config').required().description('The type of the query.'),
-    }).description('The config query retrieves the current configuration of the flowR instance.')
+    }).description('The config query retrieves the current configuration of the flowR instance.'),
+    flattenInvolvedNodes: () => []
 };
 //# sourceMappingURL=config-query-format.js.map

package/queries/catalog/dataflow-lens-query/dataflow-lens-query-format.d.ts

@@ -14,7 +14,7 @@ export interface DataflowLensQueryResult extends BaseQueryResult {
 }
 export declare const DataflowLensQueryDefinition: {
     readonly executor: typeof executeDataflowLensQuery;
-    readonly asciiSummarizer: (formatter: import("../../../util/ansi").OutputFormatter, _processed: import("../../../core/steps/pipeline/pipeline").PipelineOutput<import("../../../core/steps/pipeline/pipeline").Pipeline<{
+    readonly asciiSummarizer: (formatter: import("../../../util/text/ansi").OutputFormatter, _processed: import("../../../core/steps/pipeline/pipeline").PipelineOutput<import("../../../core/steps/pipeline/pipeline").Pipeline<{
         readonly name: "parse";
         readonly humanReadableName: "parse with R shell";
         readonly description: "Parse the given R code into an AST";
@@ -69,4 +69,5 @@ export declare const DataflowLensQueryDefinition: {
         readonly dependencies: readonly ["normalize"];
     }>>, queryResults: BaseQueryResult, result: string[]) => true;
     readonly schema: Joi.ObjectSchema<any>;
+    readonly flattenInvolvedNodes: () => never[];
 };

package/queries/catalog/dataflow-lens-query/dataflow-lens-query-format.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DataflowLensQueryDefinition = void 0;
 const dataflow_lens_query_executor_1 = require("./dataflow-lens-query-executor");
-const ansi_1 = require("../../../util/ansi");
-const time_1 = require("../../../util/time");
+const ansi_1 = require("../../../util/text/ansi");
+const time_1 = require("../../../util/text/time");
 const dfg_1 = require("../../../util/mermaid/dfg");
 const joi_1 = __importDefault(require("joi"));
 exports.DataflowLensQueryDefinition = {
@@ -19,6 +19,7 @@ exports.DataflowLensQueryDefinition = {
     },
     schema: joi_1.default.object({
         type: joi_1.default.string().valid('dataflow-lens').required().description('The type of the query.'),
-    }).description('The dataflow-lens query returns a simplified view on the dataflow graph')
+    }).description('The dataflow-lens query returns a simplified view on the dataflow graph'),
+    flattenInvolvedNodes: () => []
 };
 //# sourceMappingURL=dataflow-lens-query-format.js.map

package/queries/catalog/dataflow-query/dataflow-query-format.d.ts

@@ -2,6 +2,7 @@ import type { BaseQueryFormat, BaseQueryResult } from '../../base-query-format';
 import type { DataflowGraph } from '../../../dataflow/graph/graph';
 import { executeDataflowQuery } from './dataflow-query-executor';
 import Joi from 'joi';
+import type { NodeId } from '../../../r-bridge/lang-4.x/ast/model/processing/node-id';
 /**
  * Simple re-returns the dataflow graph of the analysis.
  */
@@ -14,7 +15,7 @@ export interface DataflowQueryResult extends BaseQueryResult {
 }
 export declare const DataflowQueryDefinition: {
     readonly executor: typeof executeDataflowQuery;
-    readonly asciiSummarizer: (formatter: import("../../../util/ansi").OutputFormatter, _processed: import("../../../core/steps/pipeline/pipeline").PipelineOutput<import("../../../core/steps/pipeline/pipeline").Pipeline<{
+    readonly asciiSummarizer: (formatter: import("../../../util/text/ansi").OutputFormatter, _processed: import("../../../core/steps/pipeline/pipeline").PipelineOutput<import("../../../core/steps/pipeline/pipeline").Pipeline<{
         readonly name: "parse";
         readonly humanReadableName: "parse with R shell";
         readonly description: "Parse the given R code into an AST";
@@ -69,4 +70,5 @@ export declare const DataflowQueryDefinition: {
         readonly dependencies: readonly ["normalize"];
     }>>, queryResults: BaseQueryResult, result: string[]) => true;
     readonly schema: Joi.ObjectSchema<any>;
+    readonly flattenInvolvedNodes: (queryResults: BaseQueryResult) => NodeId[];
 };

package/queries/catalog/dataflow-query/dataflow-query-format.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DataflowQueryDefinition = void 0;
 const dataflow_query_executor_1 = require("./dataflow-query-executor");
-const ansi_1 = require("../../../util/ansi");
-const time_1 = require("../../../util/time");
+const ansi_1 = require("../../../util/text/ansi");
+const time_1 = require("../../../util/text/time");
 const dfg_1 = require("../../../util/mermaid/dfg");
 const joi_1 = __importDefault(require("joi"));
 exports.DataflowQueryDefinition = {
@@ -19,6 +19,14 @@ exports.DataflowQueryDefinition = {
     },
     schema: joi_1.default.object({
         type: joi_1.default.string().valid('dataflow').required().description('The type of the query.'),
-    }).description('The dataflow query simply returns the dataflow graph, there is no need to pass it multiple times!')
+    }).description('The dataflow query simply returns the dataflow graph, there is no need to pass it multiple times!'),
+    flattenInvolvedNodes: queryResults => {
+        const flattened = [];
+        const out = queryResults;
+        for (const id of out.graph.idMap?.keys() ?? []) {
+            flattened.push(id);
+        }
+        return flattened;
+    }
 };
 //# sourceMappingURL=dataflow-query-format.js.map

package/queries/catalog/dependencies-query/dependencies-query-executor.js

@@ -17,6 +17,7 @@ const source_functions_1 = require("./function-info/source-functions");
 const read_functions_1 = require("./function-info/read-functions");
 const write_functions_1 = require("./function-info/write-functions");
 const function_info_1 = require("./function-info/function-info");
+const identify_link_to_last_call_relation_1 = require("../call-context-query/identify-link-to-last-call-relation");
 function collectNamespaceAccesses(data, libraries) {
     /* for libraries, we have to additionally track all uses of `::` and `:::`, for this we currently simply traverse all uses */
     (0, visitor_1.visitAst)(data.ast.ast, n => {
@@ -96,6 +97,7 @@ function makeCallContextQuery(functions, kind) {
     return functions.map(f => ({
         type: 'call-context',
         callName: f.name,
+        callTargets: identify_link_to_last_call_relation_1.CallTargets.MustIncludeGlobal,
         includeAliases: false,
         callNameExact: true,
         subkind: f.name,
@@ -279,9 +281,9 @@ function getArgumentValue(data, vertex, argumentIndex, argumentName, resolveValu
     return undefined;
 }
 function getFunctionsToCheck(customFunctions, ignoreDefaultFunctions, defaultFunctions) {
-    const functions = ignoreDefaultFunctions ? [] : [...defaultFunctions];
+    let functions = ignoreDefaultFunctions ? [] : [...defaultFunctions];
     if (customFunctions) {
-        functions.push(...customFunctions);
+        functions = functions.concat(customFunctions);
     }
     return functions;
 }