@eagleoutice/flowr 2.2.14 → 2.2.16

package/queries/query.d.ts

@@ -23,7 +23,8 @@ import type { ProjectQuery } from './catalog/project-query/project-query-format'
 import type { OriginQuery } from './catalog/origin-query/origin-query-format';
 import type { LinterQuery } from './catalog/linter-query/linter-query-format';
 import type { NodeId } from '../r-bridge/lang-4.x/ast/model/processing/node-id';
-export type Query = CallContextQuery | ConfigQuery | SearchQuery | DataflowQuery | DataflowLensQuery | NormalizedAstQuery | IdMapQuery | DataflowClusterQuery | StaticSliceQuery | LineageQuery | DependenciesQuery | LocationMapQuery | HappensBeforeQuery | ResolveValueQuery | ProjectQuery | OriginQuery | LinterQuery;
+import type { ControlFlowQuery } from './catalog/control-flow-query/control-flow-query-format';
+export type Query = CallContextQuery | ConfigQuery | SearchQuery | DataflowQuery | ControlFlowQuery | DataflowLensQuery | NormalizedAstQuery | IdMapQuery | DataflowClusterQuery | StaticSliceQuery | LineageQuery | DependenciesQuery | LocationMapQuery | HappensBeforeQuery | ResolveValueQuery | ProjectQuery | OriginQuery | LinterQuery;
 export type QueryArgumentsWithType<QueryType extends BaseQueryFormat['type']> = Query & {
     type: QueryType;
 };
@@ -54,6 +55,65 @@ export declare const SupportedQueries: {
         readonly schema: Joi.ObjectSchema<any>;
         readonly flattenInvolvedNodes: () => never[];
     };
+    readonly 'control-flow': {
+        readonly executor: typeof import("./catalog/control-flow-query/control-flow-query-executor").executeControlFlowQuery;
+        readonly asciiSummarizer: (formatter: OutputFormatter, processed: 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";
+            readonly processor: (_results: unknown, input: Partial<import("../r-bridge/parser").ParseRequiredInput<string>>) => Promise<import("../r-bridge/parser").ParseStepOutput<string>>;
+            readonly executed: import("../core/steps/pipeline-step").PipelineStepStage.OncePerFile;
+            readonly printer: {
+                readonly 0: typeof import("../core/print/print").internalPrinter;
+                readonly 2: {
+                    (value: any, replacer?: (this: any, key: string, value: any) => any, space?: string | number): string;
+                    (value: any, replacer?: (number | string)[] | null, space?: string | number): string;
+                };
+                readonly 5: ({ parsed }: import("../r-bridge/parser").ParseStepOutput<string>, config: import("../util/quads").QuadSerializationConfiguration) => string;
+            };
+            readonly dependencies: readonly [];
+            readonly requiredInput: import("../r-bridge/parser").ParseRequiredInput<string>;
+        } | {
+            readonly name: "normalize";
+            readonly humanReadableName: "normalize";
+            readonly description: "Normalize the AST to flowR's AST";
+            readonly processor: (results: {
+                parse?: import("../r-bridge/parser").ParseStepOutput<string>;
+            }, input: Partial<import("../core/steps/all/core/10-normalize").NormalizeRequiredInput>) => 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>>;
+            readonly executed: import("../core/steps/pipeline-step").PipelineStepStage.OncePerFile;
+            readonly printer: {
+                readonly 0: typeof import("../core/print/print").internalPrinter;
+                readonly 2: typeof import("../core/print/normalize-printer").normalizedAstToJson;
+                readonly 5: typeof import("../core/print/normalize-printer").normalizedAstToQuads;
+                readonly 3: typeof import("../core/print/normalize-printer").printNormalizedAstToMermaid;
+                readonly 4: typeof import("../core/print/normalize-printer").printNormalizedAstToMermaidUrl;
+            };
+            readonly dependencies: readonly ["parse"];
+            readonly requiredInput: import("../core/steps/all/core/10-normalize").NormalizeRequiredInput;
+        } | {
+            readonly humanReadableName: "dataflow";
+            readonly processor: (results: {
+                normalize?: import("../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+            }, input: {
+                request?: import("../r-bridge/retriever").RParseRequests;
+                parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
+            readonly requiredInput: {};
+            readonly name: "dataflow";
+            readonly description: "Construct the dataflow graph";
+            readonly executed: import("../core/steps/pipeline-step").PipelineStepStage.OncePerFile;
+            readonly printer: {
+                readonly 0: typeof import("../core/print/print").internalPrinter;
+                readonly 2: typeof import("../core/print/dataflow-printer").dataflowGraphToJson;
+                readonly 5: typeof import("../core/print/dataflow-printer").dataflowGraphToQuads;
+                readonly 3: typeof import("../core/print/dataflow-printer").dataflowGraphToMermaid;
+                readonly 4: typeof import("../core/print/dataflow-printer").dataflowGraphToMermaidUrl;
+            };
+            readonly dependencies: readonly ["normalize"];
+        }>>, queryResults: BaseQueryResult, result: string[]) => true;
+        readonly schema: Joi.ObjectSchema<any>;
+        readonly flattenInvolvedNodes: (queryResults: BaseQueryResult) => NodeId[];
+    };
     readonly dataflow: {
         readonly executor: typeof import("./catalog/dataflow-query/dataflow-query-executor").executeDataflowQuery;
         readonly asciiSummarizer: (formatter: OutputFormatter, _processed: PipelineOutput<import("../core/steps/pipeline/pipeline").Pipeline<{
@@ -96,7 +156,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -155,7 +215,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -214,7 +274,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -273,7 +333,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -332,7 +392,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -391,7 +451,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -450,7 +510,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -509,7 +569,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -574,7 +634,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -633,7 +693,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -692,7 +752,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -751,7 +811,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -810,7 +870,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";
@@ -869,7 +929,7 @@ export declare const SupportedQueries: {
             }, input: {
                 request?: import("../r-bridge/retriever").RParseRequests;
                 parser?: import("../r-bridge/parser").Parser<import("../r-bridge/parser").KnownParserType>;
-            }) => import("../dataflow/info").DataflowInformation;
+            }, config: import("../config").FlowrConfigOptions) => import("../dataflow/info").DataflowInformation;
             readonly requiredInput: {};
             readonly name: "dataflow";
             readonly description: "Construct the dataflow graph";

package/queries/query.js

@@ -30,9 +30,11 @@ const dataflow_lens_query_format_1 = require("./catalog/dataflow-lens-query/data
 const project_query_format_1 = require("./catalog/project-query/project-query-format");
 const origin_query_format_1 = require("./catalog/origin-query/origin-query-format");
 const linter_query_format_1 = require("./catalog/linter-query/linter-query-format");
+const control_flow_query_format_1 = require("./catalog/control-flow-query/control-flow-query-format");
 exports.SupportedQueries = {
     'call-context': call_context_query_format_1.CallContextQueryDefinition,
     'config': config_query_format_1.ConfigQueryDefinition,
+    'control-flow': control_flow_query_format_1.ControlFlowQueryDefinition,
     'dataflow': dataflow_query_format_1.DataflowQueryDefinition,
     'dataflow-lens': dataflow_lens_query_format_1.DataflowLensQueryDefinition,
     'id-map': id_map_query_format_1.IdMapQueryDefinition,

package/r-bridge/lang-4.x/ast/parser/json/parser.d.ts

@@ -2,6 +2,7 @@ import type { IdGenerator, NormalizedAst } from '../../model/processing/decorate
 import type { NoInfo, RNode } from '../../model/model';
 import type { ParseStepOutputTS } from '../../../../../core/steps/all/core/01-parse-tree-sitter';
 import type { ParseStepOutput } from '../../../../parser';
+import type { FlowrConfigOptions } from '../../../../../config';
 export declare const parseLog: import("tslog").Logger<import("tslog").ILogObj>;
 /**
  * Take the output as produced by the parse step and normalize the AST from the R parser.
@@ -18,4 +19,4 @@ export declare function normalizeButNotDecorated({ parsed }: ParseStepOutput<str
 /**
  * Tree-Sitter pendant to {@link normalize}.
  */
-export declare function normalizeTreeSitter({ parsed }: ParseStepOutputTS, getId?: IdGenerator<NoInfo>, file?: string): NormalizedAst;
+export declare function normalizeTreeSitter({ parsed }: ParseStepOutputTS, getId: IdGenerator<NoInfo> | undefined, config: FlowrConfigOptions, file?: string): NormalizedAst;

package/r-bridge/lang-4.x/ast/parser/json/parser.js

@@ -9,6 +9,7 @@ const log_1 = require("../../../../../util/log");
 const decorate_1 = require("../../model/processing/decorate");
 const normalize_root_1 = require("../main/internal/structure/normalize-root");
 const tree_sitter_normalize_1 = require("../../../tree-sitter/tree-sitter-normalize");
+const config_1 = require("../../../../../config");
 exports.parseLog = log_1.log.getSubLogger({ name: 'ast-parser' });
 /**
  * Take the output as produced by the parse step and normalize the AST from the R parser.
@@ -31,8 +32,9 @@ function normalizeButNotDecorated({ parsed }) {
 /**
  * Tree-Sitter pendant to {@link normalize}.
  */
-function normalizeTreeSitter({ parsed }, getId = (0, decorate_1.deterministicCountingIdGenerator)(0), file) {
-    const result = (0, decorate_1.decorateAst)((0, tree_sitter_normalize_1.normalizeTreeSitterTreeToAst)(parsed), { getId, file });
+function normalizeTreeSitter({ parsed }, getId = (0, decorate_1.deterministicCountingIdGenerator)(0), config, file) {
+    const lax = (0, config_1.getEngineConfig)(config, 'tree-sitter')?.lax;
+    const result = (0, decorate_1.decorateAst)((0, tree_sitter_normalize_1.normalizeTreeSitterTreeToAst)(parsed, lax), { getId, file });
     result.hasError = parsed.rootNode.hasError;
     return result;
 }

package/r-bridge/lang-4.x/convert-values.js

@@ -7,6 +7,7 @@ exports.boolean2ts = boolean2ts;
 exports.number2ts = number2ts;
 exports.string2ts = string2ts;
 exports.isNA = isNA;
+const strings_1 = require("../../util/text/strings");
 class ValueConversionError extends Error {
     constructor(message) {
         super(message);
@@ -136,7 +137,7 @@ function string2ts(value) {
         const flags = value[1];
         if (flags === '"' || flags === '\'') {
             return {
-                str: value.slice(2, -1),
+                str: (0, strings_1.dropRawStringSurround)(value.slice(2, -1)),
                 quotes: flags,
                 flag: 'raw'
             };

package/r-bridge/lang-4.x/tree-sitter/tree-sitter-executor.d.ts

@@ -1,6 +1,7 @@
 import Parser from 'web-tree-sitter';
 import type { RParseRequest } from '../../retriever';
 import type { SyncParser } from '../../parser';
+import type { TreeSitterEngineConfig } from '../../../config';
 export declare const DEFAULT_TREE_SITTER_R_WASM_PATH = "./node_modules/@eagleoutice/tree-sitter-r/tree-sitter-r.wasm";
 export declare const DEFAULT_TREE_SITTER_WASM_PATH = "./node_modules/web-tree-sitter/tree-sitter.wasm";
 /**
@@ -12,10 +13,11 @@ export declare class TreeSitterExecutor implements SyncParser<Parser.Tree> {
     private static language;
     /**
      * Initializes the underlying tree-sitter parser. This only needs to be called once globally.
+     * @param config - The configuration for the tree-sitter engine, which can include paths to the wasm files.
      * @param overrideWasmPath - The path to the tree-sitter-r wasm file, which takes precedence over the config and default paths if set.
      * @param overrideTreeSitterWasmPath - The path to the tree-sitter wasm file, which takes precedence over the config and default paths if set.
      */
-    static initTreeSitter(overrideWasmPath?: string, overrideTreeSitterWasmPath?: string): Promise<void>;
+    static initTreeSitter(config?: TreeSitterEngineConfig, overrideWasmPath?: string, overrideTreeSitterWasmPath?: string): Promise<void>;
     constructor();
     rVersion(): Promise<string | 'unknown' | 'none'>;
     treeSitterVersion(): number;

package/r-bridge/lang-4.x/tree-sitter/tree-sitter-executor.js

@@ -6,7 +6,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.TreeSitterExecutor = exports.DEFAULT_TREE_SITTER_WASM_PATH = exports.DEFAULT_TREE_SITTER_R_WASM_PATH = void 0;
 const web_tree_sitter_1 = __importDefault(require("web-tree-sitter"));
 const fs_1 = __importDefault(require("fs"));
-const config_1 = require("../../../config");
 const log_1 = require("../../../util/log");
 exports.DEFAULT_TREE_SITTER_R_WASM_PATH = './node_modules/@eagleoutice/tree-sitter-r/tree-sitter-r.wasm';
 exports.DEFAULT_TREE_SITTER_WASM_PATH = './node_modules/web-tree-sitter/tree-sitter.wasm';
@@ -20,11 +19,12 @@ class TreeSitterExecutor {
     static language;
     /**
      * Initializes the underlying tree-sitter parser. This only needs to be called once globally.
+     * @param config - The configuration for the tree-sitter engine, which can include paths to the wasm files.
      * @param overrideWasmPath - The path to the tree-sitter-r wasm file, which takes precedence over the config and default paths if set.
      * @param overrideTreeSitterWasmPath - The path to the tree-sitter wasm file, which takes precedence over the config and default paths if set.
      */
-    static async initTreeSitter(overrideWasmPath, overrideTreeSitterWasmPath) {
-        const treeSitterWasmPath = overrideTreeSitterWasmPath ?? (0, config_1.getEngineConfig)('tree-sitter')?.treeSitterWasmPath ?? exports.DEFAULT_TREE_SITTER_WASM_PATH;
+    static async initTreeSitter(config, overrideWasmPath, overrideTreeSitterWasmPath) {
+        const treeSitterWasmPath = overrideTreeSitterWasmPath ?? config?.treeSitterWasmPath ?? exports.DEFAULT_TREE_SITTER_WASM_PATH;
         // noinspection JSUnusedGlobalSymbols - this is used by emscripten, see https://emscripten.org/docs/api_reference/module.html
         await web_tree_sitter_1.default.init({
             locateFile: treeSitterWasmPath ? (path, prefix) => {
@@ -38,7 +38,7 @@ class TreeSitterExecutor {
             print: (s) => wasmLog.debug(s),
             printErr: (s) => wasmLog.error(s)
         });
-        const wasmPath = overrideWasmPath ?? (0, config_1.getEngineConfig)('tree-sitter')?.wasmPath ?? exports.DEFAULT_TREE_SITTER_R_WASM_PATH;
+        const wasmPath = overrideWasmPath ?? config?.wasmPath ?? exports.DEFAULT_TREE_SITTER_R_WASM_PATH;
         TreeSitterExecutor.language = await web_tree_sitter_1.default.Language.load(wasmPath);
     }
     constructor() {

package/r-bridge/lang-4.x/tree-sitter/tree-sitter-normalize.d.ts

@@ -3,6 +3,6 @@ import type { Tree } from 'web-tree-sitter';
 /**
  * @param tree - The tree to normalize
  */
-export declare function normalizeTreeSitterTreeToAst(tree: Tree): RExpressionList;
+export declare function normalizeTreeSitterTreeToAst(tree: Tree, lax?: boolean): RExpressionList;
 export declare function makeTreeSitterLax(): void;
 export declare function makeTreeSitterStrict(): void;

package/r-bridge/lang-4.x/tree-sitter/tree-sitter-normalize.js

@@ -12,13 +12,11 @@ const normalize_meta_1 = require("../ast/parser/main/normalize-meta");
 const arrays_1 = require("../../../util/collections/arrays");
 const r_function_call_1 = require("../ast/model/nodes/r-function-call");
 const strings_1 = require("../../../util/text/strings");
-const config_1 = require("../../../config");
 const log_1 = require("../../../util/log");
 /**
  * @param tree - The tree to normalize
  */
-function normalizeTreeSitterTreeToAst(tree) {
-    const lax = (0, config_1.getEngineConfig)('tree-sitter')?.lax;
+function normalizeTreeSitterTreeToAst(tree, lax) {
     if (lax) {
         makeTreeSitterLax();
     }
@@ -293,13 +291,20 @@ function convertTreeNode(node) {
                     ...defaultInfo
                 };
             }
-            const args = (0, arrays_1.splitArrayOn)(nonErrorChildren(argsParentheses).slice(1, -1), x => x.type === 'comma');
+            const rawArgs = nonErrorChildren(argsParentheses);
+            const [comments, noCommentrawArgs] = splitComments(rawArgs);
+            const args = (0, arrays_1.splitArrayOn)(noCommentrawArgs.slice(1, -1), x => x.type === 'comma');
             const funcRange = makeSourceRange(func);
+            const mappedArgs = args.map(n => n.length == 0 ? r_function_call_1.EmptyArgument : convertTreeNode(n[0]));
             const call = {
-                arguments: args.map(n => n.length == 0 ? r_function_call_1.EmptyArgument : convertTreeNode(n[0])),
+                arguments: mappedArgs,
                 location: funcRange,
                 lexeme: func.text,
-                ...defaultInfo
+                ...defaultInfo,
+                info: {
+                    ...defaultInfo.info,
+                    additionalTokens: comments.map(c => c[1]),
+                }
             };
             if (func.type === tree_sitter_types_1.TreeSitterType.Identifier || func.type === tree_sitter_types_1.TreeSitterType.String || func.type === tree_sitter_types_1.TreeSitterType.NamespaceOperator || func.type === tree_sitter_types_1.TreeSitterType.Return) {
                 let funcNode = convertTreeNode(func);
@@ -336,14 +341,18 @@ function convertTreeNode(node) {
         }
         case tree_sitter_types_1.TreeSitterType.FunctionDefinition: {
             const [name, paramsParens, body] = nonErrorChildren(node);
-            const params = (0, arrays_1.splitArrayOn)(paramsParens.children.slice(1, -1), x => x.type === 'comma');
+            const [comments, noCommentRawParams] = splitComments(paramsParens.children.slice(1, -1));
+            const params = (0, arrays_1.splitArrayOn)(noCommentRawParams, x => x.type === 'comma');
             return {
                 type: type_1.RType.FunctionDefinition,
                 parameters: params.map(n => convertTreeNode(n[0])),
                 body: (0, normalize_meta_1.ensureExpressionList)(convertTreeNode(body)),
                 location: makeSourceRange(name),
                 lexeme: name.text,
-                ...defaultInfo
+                info: {
+                    ...defaultInfo.info,
+                    additionalTokens: comments.map(c => c[1]),
+                }
             };
         }
         case tree_sitter_types_1.TreeSitterType.String:
@@ -491,7 +500,7 @@ function convertTreeNode(node) {
                 const nameRange = makeSourceRange(nameNode);
                 return {
                     type: type_1.RType.Argument,
-                    name: name,
+                    name,
                     value: valueNode ? convertTreeNode(valueNode) : undefined,
                     location: nameRange,
                     lexeme: nameNode.text,

package/r-bridge/shell.d.ts

@@ -1,6 +1,7 @@
 import { type MergeableRecord } from '../util/objects';
 import type { SemVer } from 'semver';
 import type { AsyncOrSync } from 'ts-essentials';
+import type { RShellEngineConfig } from '../config';
 import type { AsyncParser } from './parser';
 import type { RParseRequest } from './retriever';
 export type OutputStreamSelector = 'stdout' | 'stderr' | 'both';
@@ -68,7 +69,7 @@ export interface RShellOptions extends RShellSessionOptions {
     readonly sessionName: string;
 }
 export declare const DEFAULT_R_PATH: string;
-export declare function getDefaultRShellOptions(): RShellOptions;
+export declare function getDefaultRShellOptions(config?: RShellEngineConfig): RShellOptions;
 /**
  * The `RShell` represents an interactive session with the R interpreter.
  * You can configure it by {@link RShellOptions}.
@@ -85,7 +86,7 @@ export declare class RShell implements AsyncParser<string> {
     private readonly log;
     private versionCache;
     private tempDirs;
-    constructor(options?: Partial<RShellOptions>);
+    constructor(config?: RShellEngineConfig, options?: Partial<RShellOptions>);
     parse(request: RParseRequest): Promise<string>;
     private revive;
     /**

package/r-bridge/shell.js

@@ -46,7 +46,6 @@ const preload_1 = __importDefault(require("semver/preload"));
 const os_1 = require("../util/os");
 const fs_1 = __importDefault(require("fs"));
 const init_1 = require("./init");
-const config_1 = require("../config");
 const convert_values_1 = require("./lang-4.x/convert-values");
 const retriever_1 = require("./retriever");
 exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = {
@@ -62,10 +61,10 @@ exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = {
 };
 exports.DEFAULT_R_PATH = (0, os_1.getPlatform)() === 'windows' ? 'R.exe' : 'R';
 let DEFAULT_R_SHELL_OPTIONS = undefined;
-function getDefaultRShellOptions() {
+function getDefaultRShellOptions(config) {
     if (!DEFAULT_R_SHELL_OPTIONS) {
         DEFAULT_R_SHELL_OPTIONS = {
-            pathToRExecutable: (0, config_1.getEngineConfig)('r-shell')?.rPath ?? exports.DEFAULT_R_PATH,
+            pathToRExecutable: config?.rPath ?? exports.DEFAULT_R_PATH,
             // -s is a short form of --no-echo (and the old version --slave), but this one works in R 3 and 4
             // (see https://github.com/wch/r-source/commit/f1ff49e74593341c74c20de9517f31a22c8bcb04)
             commandLineOptions: ['--vanilla', '--quiet', '--no-save', '-s'],
@@ -97,8 +96,8 @@ class RShell {
     versionCache = null;
     // should never be more than one, but let's be sure
     tempDirs = new Set();
-    constructor(options) {
-        this.options = { ...getDefaultRShellOptions(), ...options };
+    constructor(config, options) {
+        this.options = { ...getDefaultRShellOptions(config), ...options };
         this.log = log_1.log.getSubLogger({ name: this.options.sessionName });
         this.session = new RShellSession(this.options, this.log);
         this.revive();

package/search/flowr-search-builder.d.ts

@@ -1,6 +1,6 @@
 import type { NodeId } from '../r-bridge/lang-4.x/ast/model/processing/node-id';
 import type { FlowrSearchElement, FlowrSearchElementFromQuery, FlowrSearchElements, FlowrSearchGetFilter } from './flowr-search';
-import type { FlowrFilterExpression } from './flowr-search-filters';
+import type { FlowrFilter, FlowrFilterExpression } from './flowr-search-filters';
 import type { FlowrSearchGeneratorNode, GeneratorNames } from './search-executor/search-generators';
 import type { FlowrSearchTransformerNode, GetOutputOfTransformer, TransformerNames } from './search-executor/search-transformer';
 import type { SlicingCriteria } from '../slicing/criterion/parse';
@@ -155,7 +155,7 @@ export declare class FlowrSearchBuilder<Generator extends GeneratorNames, Transf
     /**
      * only returns the elements that match the given filter.
      */
-    filter(filter: FlowrFilterExpression): FlowrSearchBuilderOut<Generator, Transformers, Info, 'filter'>;
+    filter<Filter extends FlowrFilter>(filter: FlowrFilterExpression<Filter>): FlowrSearchBuilderOut<Generator, Transformers, Info, 'filter'>;
     /**
      * first either returns the first element of the search or nothing, if no elements are present.
      */
@@ -201,6 +201,10 @@ export declare class FlowrSearchBuilder<Generator extends GeneratorNames, Transf
      * merge combines the search results with those of another search.
      */
     merge<Generator2 extends GeneratorNames, Transformers2 extends TransformerNames[], OtherElementType extends FlowrSearchElements<Info, FlowrSearchElement<Info>[]>>(other: FlowrSearchBuilder<Generator2, Transformers2, Info, OtherElementType>): FlowrSearchBuilder<Generator, Transformers, Info>;
+    /**
+     * Removes duplicate elements based on the ids of the elements.
+     */
+    unique(): FlowrSearchBuilderOut<Generator, Transformers, Info, 'unique'>;
     /**
      * Construct the final search (this may happen automatically with most search handlers).
      *

package/search/flowr-search-builder.js

@@ -195,6 +195,13 @@ class FlowrSearchBuilder {
         this.search.push({ type: 'transformer', name: 'merge', args: { generator: other.generator, search: other.search } });
         return this;
     }
+    /**
+     * Removes duplicate elements based on the ids of the elements.
+     */
+    unique() {
+        this.search.push({ type: 'transformer', name: 'unique', args: undefined });
+        return this;
+    }
     /**
      * Construct the final search (this may happen automatically with most search handlers).
      *

package/search/flowr-search-filters.d.ts

@@ -2,23 +2,47 @@ import { RType } from '../r-bridge/lang-4.x/ast/model/type';
 import type { VertexType } from '../dataflow/graph/vertex';
 import type { NormalizedAst, ParentInformation } from '../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { DataflowInformation } from '../dataflow/info';
-import type { RNode } from '../r-bridge/lang-4.x/ast/model/model';
+import type { FlowrSearchElement } from './flowr-search';
+import type { MergeableRecord } from '../util/objects';
+import type { Enrichment } from './search-executor/search-enrichers';
 export type FlowrFilterName = keyof typeof FlowrFilters;
+interface FlowrFilterWithArgs<Filter extends FlowrFilterName, Args extends FlowrFilterArgs<Filter>> {
+    name: Filter;
+    args: Args;
+}
 export declare enum FlowrFilter {
-    DropEmptyArguments = "drop-empty-arguments"
+    /**
+     * Drops search elements that represent empty arguments. Specifically, all nodes that are arguments and have an undefined name are skipped.
+     * This filter does not accept any arguments.
+     */
+    DropEmptyArguments = "drop-empty-arguments",
+    /**
+     * Only returns search elements whose enrichments' JSON representations match a given test regular expression.
+     * This filter accepts {@link MatchesEnrichmentArgs}, which includes the enrichment to match for, as well as the regular expression to test the enrichment's (non-pretty-printed) JSON representation for.
+     * To test for included function names in an enrichment like {@link Enrichment.CallTargets}, the helper function {@link testFunctionsIgnoringPackage} can be used.
+     */
+    MatchesEnrichment = "matches-enrichment"
 }
+export type FlowrFilterFunction<T extends MergeableRecord> = (e: FlowrSearchElement<ParentInformation>, args: T) => boolean;
 export declare const ValidFlowrFilters: Set<string>;
 export declare const ValidFlowrFiltersReverse: {
     [k: string]: string;
 };
 export declare const FlowrFilters: {
-    readonly "drop-empty-arguments": (n: RNode<ParentInformation>) => boolean;
+    readonly "drop-empty-arguments": (e: FlowrSearchElement<ParentInformation>, _args: never) => boolean;
+    readonly "matches-enrichment": (e: FlowrSearchElement<ParentInformation>, args: MatchesEnrichmentArgs<Enrichment>) => boolean;
 };
-type ValidFilterTypes = FlowrFilterName | RType | VertexType;
+export type FlowrFilterArgs<F extends FlowrFilter> = typeof FlowrFilters[F] extends FlowrFilterFunction<infer Args> ? Args : never;
+export interface MatchesEnrichmentArgs<E extends Enrichment> extends MergeableRecord {
+    enrichment: E;
+    test: RegExp;
+}
+export declare function testFunctionsIgnoringPackage(functions: string[]): RegExp;
+type ValidFilterTypes<F extends FlowrFilter = FlowrFilter> = FlowrFilterName | FlowrFilterWithArgs<F, FlowrFilterArgs<F>> | RType | VertexType;
 /**
  * By default, we provide filter for every {@link RType} and {@link VertexType}.
  */
-export type FlowrFilterExpression = FlowrFilterCombinator | ValidFilterTypes;
+export type FlowrFilterExpression<F extends FlowrFilter = FlowrFilter> = FlowrFilterCombinator | ValidFilterTypes<F>;
 interface BooleanBinaryNode<Composite> {
     readonly type: 'and' | 'or' | 'xor';
     readonly left: Composite;
@@ -38,7 +62,7 @@ type LeafVertexType = {
 };
 type LeafSpecial = {
     readonly type: 'special';
-    readonly value: string;
+    readonly value: FlowrFilterName | FlowrFilterWithArgs<FlowrFilter, FlowrFilterArgs<FlowrFilter>>;
 };
 type Leaf = LeafRType | LeafVertexType | LeafSpecial;
 type BooleanNode = BooleanBinaryNode<BooleanNode> | BooleanUnaryNode<BooleanNode> | Leaf;
@@ -66,9 +90,9 @@ export declare function isBinaryTree(tree: unknown): tree is {
     tree: BooleanNode;
 };
 interface FilterData {
-    readonly node: RNode<ParentInformation>;
+    readonly element: FlowrSearchElement<ParentInformation>;
     readonly normalize: NormalizedAst;
     readonly dataflow: DataflowInformation;
 }
-export declare function evalFilter(filter: FlowrFilterExpression, data: FilterData): boolean;
+export declare function evalFilter<Filter extends FlowrFilter>(filter: FlowrFilterExpression<Filter>, data: FilterData): boolean;
 export {};