@eagleoutice/flowr 2.2.14 → 2.2.15

package/dataflow/graph/unknown-replacement.js

@@ -0,0 +1,12 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.onReplacementOperator = onReplacementOperator;
+exports.handleReplacementOperator = handleReplacementOperator;
+const handlers = [];
+function onReplacementOperator(handler) {
+    handlers.push(handler);
+}
+function handleReplacementOperator(args) {
+    handlers.forEach(handler => handler(args));
+}
+//# sourceMappingURL=unknown-replacement.js.map

package/dataflow/graph/unknown-side-effect.d.ts

@@ -0,0 +1,7 @@
+import type { LinkTo } from '../../queries/catalog/call-context-query/call-context-query-format';
+import type { NodeId } from '../../r-bridge/lang-4.x/ast/model/processing/node-id';
+import type { REnvironmentInformation } from '../environments/environment';
+import type { DataflowGraph } from './graph';
+export type UnknownSideEffectHandler = (graph: DataflowGraph, env: REnvironmentInformation, id: NodeId, target?: LinkTo<RegExp | string>) => void;
+export declare function onUnknownSideEffect(handler: UnknownSideEffectHandler): void;
+export declare function handleUnknownSideEffect(graph: DataflowGraph, env: REnvironmentInformation, id: NodeId, target?: LinkTo<RegExp | string>): void;

package/dataflow/graph/unknown-side-effect.js

@@ -0,0 +1,13 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.onUnknownSideEffect = onUnknownSideEffect;
+exports.handleUnknownSideEffect = handleUnknownSideEffect;
+const handlers = [];
+function onUnknownSideEffect(handler) {
+    handlers.push(handler);
+}
+function handleUnknownSideEffect(graph, env, id, target) {
+    graph.markIdForUnknownSideEffects(id, target);
+    handlers.forEach(handler => handler(graph, env, id, target));
+}
+//# sourceMappingURL=unknown-side-effect.js.map

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

@@ -10,7 +10,10 @@ const edge_1 = require("../../../../../graph/edge");
 const identifier_1 = require("../../../../../environments/identifier");
 const resolve_by_name_1 = require("../../../../../environments/resolve-by-name");
 const unnamed_call_handling_1 = require("../unnamed-call-handling");
+const general_1 = require("../../../../../eval/values/general");
+const r_value_1 = require("../../../../../eval/values/r-value");
 const log_1 = require("../../../../../../util/log");
+const alias_tracking_1 = require("../../../../../eval/resolve/alias-tracking");
 function processApply(name, args, rootId, data, config) {
     const { indexOfFunction = 1, nameOfFunctionArgument, unquoteFunction, resolveInEnvironment, resolveValue } = config;
     /* as the length is one-based and the argument filter mapping is zero-based, we do not have to subtract 1 */
@@ -54,9 +57,9 @@ function processApply(name, args, rootId, data, config) {
     else if (val.type === type_1.RType.Symbol) {
         functionId = val.info.id;
         if (resolveValue) {
-            const resolved = (0, resolve_by_name_1.resolveValueOfVariable)(val.content, data.environment);
-            if (resolved?.length === 1 && typeof resolved[0] === 'string') {
-                functionName = resolved[0];
+            const resolved = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(val.info.id, { environment: data.environment, idMap: data.completeAst.idMap }));
+            if (resolved?.elements.length === 1 && resolved.elements[0].type === 'string') {
+                functionName = (0, r_value_1.isValue)(resolved.elements[0].value) ? resolved.elements[0].value.str : undefined;
             }
         }
         else {
@@ -72,7 +75,7 @@ function processApply(name, args, rootId, data, config) {
         logger_1.dataflowLogger.warn(`Expected symbol or string as function argument at index ${index}, but got ${JSON.stringify(val)} instead.`);
         return information;
     }
-    const allOtherArguments = processedArguments.filter((_, i) => i !== index).map((arg, i) => {
+    const allOtherArguments = processedArguments.map((arg, i) => {
         const counterpart = args[i];
         if (arg && counterpart !== r_function_call_1.EmptyArgument) {
             return {
@@ -85,7 +88,7 @@ function processApply(name, args, rootId, data, config) {
         else {
             return r_function_call_1.EmptyArgument;
         }
-    });
+    }).filter((_, i) => i !== index);
     if (anonymous) {
         const rootFnId = functionId;
         functionId = 'anon-' + rootFnId;

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

@@ -20,6 +20,8 @@ const containers_1 = require("../../../../../../util/containers");
 const config_1 = require("../../../../../../config");
 const named_call_handling_1 = require("../named-call-handling");
 const built_in_1 = require("../../../../../environments/built-in");
+const unknown_side_effect_1 = require("../../../../../graph/unknown-side-effect");
+const alias_tracking_1 = require("../../../../../eval/resolve/alias-tracking");
 function toReplacementSymbol(target, prefix, superAssignment) {
     return {
         type: type_1.RType.Symbol,
@@ -142,7 +144,7 @@ args, rootId, data, config) {
         name, args: effectiveArgs, rootId, data, forceArgs: config.forceArgs,
         origin: 'builtin:assignment'
     }).information;
-    info.graph.markIdForUnknownSideEffects(rootId);
+    (0, unknown_side_effect_1.handleUnknownSideEffect)(info.graph, info.environment, rootId);
     return info;
 }
 function extractSourceAndTarget(args) {
@@ -269,7 +271,7 @@ function markAsAssignment(information, nodeToDefine, sourceIds, rootIdOfAssignme
 function processAssignmentToSymbol(config) {
     const { nameOfAssignmentFunction, source, args: [targetArg, sourceArg], target, rootId, data, information, makeMaybe, quoteSource } = config;
     const referenceType = checkTargetReferenceType(source, sourceArg);
-    const aliases = (0, resolve_by_name_1.getAliases)([source.info.id], information.graph, information.environment);
+    const aliases = (0, alias_tracking_1.getAliases)([source.info.id], information.graph, information.environment);
     const writeNodes = produceWrittenNodes(rootId, targetArg, referenceType, data, makeMaybe ?? false, aliases);
     if (writeNodes.length !== 1 && log_1.log.settings.minLevel <= 4 /* LogLevel.Warn */) {
         log_1.log.warn(`Unexpected write number in assignment: ${JSON.stringify(writeNodes)}`);

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

@@ -12,9 +12,12 @@ const log_1 = require("../../../../../../util/log");
 const built_in_source_1 = require("./built-in-source");
 const edge_1 = require("../../../../../graph/edge");
 const type_1 = require("../../../../../../r-bridge/lang-4.x/ast/model/type");
-const resolve_by_name_1 = require("../../../../../environments/resolve-by-name");
 const append_1 = require("../../../../../environments/append");
 const assert_1 = require("../../../../../../util/assert");
+const general_1 = require("../../../../../eval/values/general");
+const string_constants_1 = require("../../../../../eval/values/string/string-constants");
+const unknown_side_effect_1 = require("../../../../../graph/unknown-side-effect");
+const alias_tracking_1 = require("../../../../../eval/resolve/alias-tracking");
 const arrays_1 = require("../../../../../../util/collections/arrays");
 function processEvalCall(name, args, rootId, data, config) {
     if (args.length !== 1 || args[0] === r_function_call_1.EmptyArgument || !args[0].value) {
@@ -30,7 +33,7 @@ function processEvalCall(name, args, rootId, data, config) {
     }
     if (!(0, config_1.getConfig)().solver.evalStrings) {
         (0, log_1.expensiveTrace)(logger_1.dataflowLogger, () => `Skipping eval call ${JSON.stringify(evalArgument)} (disabled in config file)`);
-        information.graph.markIdForUnknownSideEffects(rootId);
+        (0, unknown_side_effect_1.handleUnknownSideEffect)(information.graph, information.environment, rootId);
         return information;
     }
     const code = resolveEvalToCode(evalArgument.value, data.environment, data.completeAst.idMap);
@@ -62,7 +65,7 @@ function processEvalCall(name, args, rootId, data, config) {
         };
     }
     (0, log_1.expensiveTrace)(logger_1.dataflowLogger, () => `Non-constant argument ${JSON.stringify(args)} for eval is currently not supported, skipping`);
-    information.graph.markIdForUnknownSideEffects(rootId);
+    (0, unknown_side_effect_1.handleUnknownSideEffect)(information.graph, information.environment, rootId);
     return information;
 }
 function resolveEvalToCode(evalArgument, env, idMap) {
@@ -77,9 +80,9 @@ function resolveEvalToCode(evalArgument, env, idMap) {
             return [arg.value.content.str];
         }
         else if (arg.value?.type === type_1.RType.Symbol) {
-            const resolve = (0, resolve_by_name_1.resolveValueOfVariable)(arg.value.content, env, idMap);
-            if (resolve?.every(r => typeof r === 'object' && r !== null && 'str' in r)) {
-                return resolve.map(r => r.str);
+            const resolved = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(arg.value.info.id, { environment: env, idMap: idMap }));
+            if (resolved) {
+                return (0, string_constants_1.collectStrings)(resolved.elements);
             }
         }
         else if (arg.value?.type === type_1.RType.FunctionCall && arg.value.named && ['paste', 'paste0'].includes(arg.value.functionName.content)) {
@@ -104,9 +107,9 @@ function getAsString(val, env, idMap) {
         return [val.content.str];
     }
     else if (val.type === type_1.RType.Symbol) {
-        const resolved = (0, resolve_by_name_1.resolveValueOfVariable)(val.content, env, idMap);
-        if (resolved?.every(r => typeof r === 'object' && r !== null && 'str' in r)) {
-            return resolved.map(r => r.str);
+        const resolved = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(val.info.id, { environment: env, idMap: idMap }));
+        if (resolved) {
+            return (0, string_constants_1.collectStrings)(resolved.elements);
         }
     }
     return undefined;

package/dataflow/internal/process/functions/call/built-in/built-in-if-then-else.js

@@ -7,11 +7,12 @@ const known_call_handling_1 = require("../known-call-handling");
 const common_1 = require("../common");
 const unpack_argument_1 = require("../argument/unpack-argument");
 const logger_1 = require("../../../../../logger");
-const resolve_by_name_1 = require("../../../../../environments/resolve-by-name");
 const edge_1 = require("../../../../../graph/edge");
 const append_1 = require("../../../../../environments/append");
 const identifier_1 = require("../../../../../environments/identifier");
 const environment_1 = require("../../../../../environments/environment");
+const general_1 = require("../../../../../eval/values/general");
+const alias_tracking_1 = require("../../../../../eval/resolve/alias-tracking");
 function processIfThenElse(name, args, rootId, data) {
     if (args.length !== 2 && args.length !== 3) {
         logger_1.dataflowLogger.warn(`If-then-else ${name.content} has something different from 2 or 3 arguments, skipping`);
@@ -33,9 +34,9 @@ function processIfThenElse(name, args, rootId, data) {
     let then;
     let makeThenMaybe = false;
     // we should defer this to the abstract interpretation
-    const values = (0, resolve_by_name_1.resolveValueOfVariable)(condArg?.lexeme, data.environment, data.completeAst.idMap);
-    const conditionIsAlwaysFalse = values?.every(d => d === false) ?? false;
-    const conditionIsAlwaysTrue = values?.every(d => d === true) ?? false;
+    const values = (0, alias_tracking_1.resolveIdToValue)(condArg?.info.id, { environment: data.environment, idMap: data.completeAst.idMap });
+    const conditionIsAlwaysFalse = (0, general_1.valueSetGuard)(values)?.elements.every(d => d.type === 'logical' && d.value === false) ?? false;
+    const conditionIsAlwaysTrue = (0, general_1.valueSetGuard)(values)?.elements.every(d => d.type === 'logical' && d.value === true) ?? false;
     if (!conditionIsAlwaysFalse) {
         then = (0, processor_1.processDataflowFor)(thenArg, data);
         if (then.entryPoint) {

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

@@ -17,6 +17,7 @@ const unpack_argument_1 = require("../argument/unpack-argument");
 const built_in_access_1 = require("./built-in-access");
 const built_in_1 = require("../../../../../environments/built-in");
 const identifier_1 = require("../../../../../environments/identifier");
+const unknown_replacement_1 = require("../../../../../graph/unknown-replacement");
 function processReplacementFunction(name, 
 /** The last one has to be the value */
 args, rootId, data, config) {
@@ -60,9 +61,15 @@ args, rootId, data, config) {
         origin: 'builtin:replacement',
         link: config.assignRootId ? { origin: [config.assignRootId] } : undefined
     });
-    const firstArg = (0, unpack_argument_1.unpackArgument)(args[0])?.info.id;
+    const firstArg = (0, unpack_argument_1.unpackArgument)(args[0]);
+    (0, unknown_replacement_1.handleReplacementOperator)({
+        operator: name.content,
+        target: firstArg?.lexeme,
+        env: res.environment,
+        id: rootId
+    });
     if (firstArg) {
-        res.graph.addEdge(firstArg, rootId, edge_1.EdgeType.DefinedBy | edge_1.EdgeType.Reads);
+        res.graph.addEdge(firstArg.info.id, rootId, edge_1.EdgeType.DefinedBy | edge_1.EdgeType.Reads);
     }
     /* a replacement reads all of its call args as well, at least as far as I am aware of */
     for (const arg of callArgs) {

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

@@ -23,9 +23,12 @@ const log_1 = require("../../../../../../util/log");
 const fs_1 = __importDefault(require("fs"));
 const parser_1 = require("../../../../../../r-bridge/lang-4.x/ast/parser/json/parser");
 const shell_executor_1 = require("../../../../../../r-bridge/shell-executor");
-const resolve_by_name_1 = require("../../../../../environments/resolve-by-name");
 const assert_1 = require("../../../../../../util/assert");
 const path_1 = __importDefault(require("path"));
+const general_1 = require("../../../../../eval/values/general");
+const r_value_1 = require("../../../../../eval/values/r-value");
+const unknown_side_effect_1 = require("../../../../../graph/unknown-side-effect");
+const alias_tracking_1 = require("../../../../../eval/resolve/alias-tracking");
 let sourceProvider = (0, retriever_1.requestProviderFromFile)();
 function setSourceProvider(provider) {
     sourceProvider = provider;
@@ -128,7 +131,7 @@ function processSourceCall(name, args, rootId, data, config) {
     const sourceFileArgument = args[0];
     if (!config.forceFollow && (0, config_1.getConfig)().ignoreSourceCalls) {
         (0, log_1.expensiveTrace)(logger_1.dataflowLogger, () => `Skipping source call ${JSON.stringify(sourceFileArgument)} (disabled in config file)`);
-        information.graph.markIdForUnknownSideEffects(rootId);
+        (0, unknown_side_effect_1.handleUnknownSideEffect)(information.graph, information.environment, rootId);
         return information;
     }
     let sourceFile;
@@ -136,14 +139,8 @@ function processSourceCall(name, args, rootId, data, config) {
         sourceFile = [(0, retriever_1.removeRQuotes)(sourceFileArgument.lexeme)];
     }
     else if (sourceFileArgument !== r_function_call_1.EmptyArgument) {
-        sourceFile = (0, resolve_by_name_1.resolveValueOfVariable)(sourceFileArgument.value?.lexeme, data.environment, data.completeAst.idMap)?.map(x => {
-            if (typeof x === 'object' && x && 'str' in x) {
-                return x.str;
-            }
-            else {
-                return undefined;
-            }
-        }).filter(assert_1.isNotUndefined);
+        const resolved = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(sourceFileArgument.info.id, { environment: data.environment, idMap: data.completeAst.idMap }));
+        sourceFile = resolved?.elements.map(r => r.type === 'string' && (0, r_value_1.isValue)(r.value) ? r.value.str : undefined).filter(assert_1.isNotUndefined);
     }
     if (sourceFile && sourceFile.length === 1) {
         const path = (0, retriever_1.removeRQuotes)(sourceFile[0]);
@@ -158,14 +155,14 @@ function processSourceCall(name, args, rootId, data, config) {
             const findCount = data.referenceChain.filter(e => e.request === request.request && e.content === request.content).length;
             if (findCount > limit) {
                 logger_1.dataflowLogger.warn(`Found cycle (>=${limit + 1}) in dataflow analysis for ${JSON.stringify(request)}: ${JSON.stringify(data.referenceChain)}, skipping further dataflow analysis`);
-                information.graph.markIdForUnknownSideEffects(rootId);
+                (0, unknown_side_effect_1.handleUnknownSideEffect)(information.graph, information.environment, rootId);
                 return information;
             }
             return sourceRequest(rootId, request, data, information, (0, decorate_1.sourcedDeterministicCountingIdGenerator)((findCount > 0 ? findCount + '::' : '') + path, name.location));
         }
     }
     (0, log_1.expensiveTrace)(logger_1.dataflowLogger, () => `Non-constant argument ${JSON.stringify(sourceFile)} for source is currently not supported, skipping`);
-    information.graph.markIdForUnknownSideEffects(rootId);
+    (0, unknown_side_effect_1.handleUnknownSideEffect)(information.graph, information.environment, rootId);
     return information;
 }
 function sourceRequest(rootId, request, data, information, getId) {
@@ -173,7 +170,7 @@ function sourceRequest(rootId, request, data, information, getId) {
         /* check if the file exists and if not, fail */
         if (!fs_1.default.existsSync(request.content)) {
             logger_1.dataflowLogger.warn(`Failed to analyze sourced file ${JSON.stringify(request)}: file does not exist`);
-            information.graph.markIdForUnknownSideEffects(rootId);
+            (0, unknown_side_effect_1.handleUnknownSideEffect)(information.graph, information.environment, rootId);
             return information;
         }
     }
@@ -195,7 +192,7 @@ function sourceRequest(rootId, request, data, information, getId) {
     catch (e) {
         logger_1.dataflowLogger.error(`Failed to analyze sourced file ${JSON.stringify(request)}, skipping: ${e.message}`);
         logger_1.dataflowLogger.error(e.stack);
-        information.graph.markIdForUnknownSideEffects(rootId);
+        (0, unknown_side_effect_1.handleUnknownSideEffect)(information.graph, information.environment, rootId);
         return information;
     }
     // 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
@@ -229,7 +226,7 @@ function standaloneSourceFile(inputRequest, data, uniqueSourceId, information) {
     // check if the sourced file has already been dataflow analyzed, and if so, skip it
     if (data.referenceChain.find(e => e.request === request.request && e.content === request.content)) {
         logger_1.dataflowLogger.info(`Found loop in dataflow analysis for ${JSON.stringify(request)}: ${JSON.stringify(data.referenceChain)}, skipping further dataflow analysis`);
-        information.graph.markIdForUnknownSideEffects(uniqueSourceId);
+        (0, unknown_side_effect_1.handleUnknownSideEffect)(information.graph, information.environment, uniqueSourceId);
         return information;
     }
     return sourceRequest(uniqueSourceId, request, {

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

@@ -11,6 +11,8 @@ const logger_1 = require("../../../../../logger");
 const environment_1 = require("../../../../../environments/environment");
 const edge_1 = require("../../../../../graph/edge");
 const identifier_1 = require("../../../../../environments/identifier");
+const general_1 = require("../../../../../eval/values/general");
+const alias_tracking_1 = require("../../../../../eval/resolve/alias-tracking");
 function processWhileLoop(name, args, rootId, data) {
     if (args.length !== 2 || args[1] === r_function_call_1.EmptyArgument) {
         logger_1.dataflowLogger.warn(`While-Loop ${name.content} does not have 2 arguments, skipping`);
@@ -21,6 +23,13 @@ function processWhileLoop(name, args, rootId, data) {
         logger_1.dataflowLogger.warn(`While-Loop ${name.content} has empty arguments in ${JSON.stringify(args)}, skipping`);
         return (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data, origin: 'default' }).information;
     }
+    // we should defer this to the abstract interpretation
+    const values = (0, alias_tracking_1.resolveIdToValue)(unpackedArgs[0]?.info.id, { environment: data.environment, idMap: data.completeAst.idMap });
+    const conditionIsAlwaysFalse = (0, general_1.valueSetGuard)(values)?.elements.every(d => d.type === 'logical' && d.value === false) ?? false;
+    //We don't care about the body if it never executes
+    if (conditionIsAlwaysFalse) {
+        unpackedArgs.pop();
+    }
     /* we inject the cf-dependency of the while-loop after the condition */
     const { information, processedArguments } = (0, known_call_handling_1.processKnownFunctionCall)({
         name,
@@ -36,10 +45,24 @@ function processWhileLoop(name, args, rootId, data) {
         }, origin: 'builtin:while-loop'
     });
     const [condition, body] = processedArguments;
+    // If the condition is always false, we don't include the body
+    if (condition !== undefined && conditionIsAlwaysFalse) {
+        information.graph.addEdge(name.info.id, condition.entryPoint, edge_1.EdgeType.Reads);
+        return {
+            unknownReferences: [],
+            in: [{ nodeId: name.info.id, name: name.lexeme, controlDependencies: data.controlDependencies, type: identifier_1.ReferenceType.Function }],
+            out: condition.out,
+            entryPoint: name.info.id,
+            exitPoints: [],
+            graph: information.graph,
+            environment: information.environment
+        };
+    }
     (0, assert_1.guard)(condition !== undefined && body !== undefined, () => `While-Loop ${name.content} has no condition or body, impossible!`);
     const originalDependency = data.controlDependencies;
     if ((0, info_1.alwaysExits)(condition)) {
         logger_1.dataflowLogger.warn(`While-Loop ${rootId} forces exit in condition, skipping rest`);
+        information.graph.addEdge(name.info.id, condition.entryPoint, edge_1.EdgeType.Reads);
         return condition;
     }
     const remainingInputs = (0, linker_1.linkInputs)([

package/dataflow/internal/process/functions/call/known-call-handling.js

@@ -10,6 +10,7 @@ const edge_1 = require("../../../../graph/edge");
 const logger_1 = require("../../../../logger");
 const vertex_1 = require("../../../../graph/vertex");
 const log_1 = require("../../../../../util/log");
+const unknown_side_effect_1 = require("../../../../graph/unknown-side-effect");
 function markNonStandardEvaluationEdges(markAsNSE, callArgs, finalGraph, rootId) {
     for (const nse of markAsNSE) {
         if (nse < callArgs.length) {
@@ -46,7 +47,7 @@ function processKnownFunctionCall({ name, args, rootId, data, reverseOrder = fal
         origin: origin === 'default' ? ['function'] : [origin]
     });
     if (hasUnknownSideEffect) {
-        finalGraph.markIdForUnknownSideEffects(rootId);
+        (0, unknown_side_effect_1.handleUnknownSideEffect)(finalGraph, data.environment, rootId);
     }
     const inIds = remainingReadInArgs;
     const fnRef = { nodeId: rootId, name: functionCallName, controlDependencies: data.controlDependencies, type: identifier_1.ReferenceType.Function };

package/documentation/doc-util/doc-query.d.ts

@@ -1,13 +1,16 @@
 import type { RShell } from '../../r-bridge/shell';
-import type { Queries, SupportedQueryTypes } from '../../queries/query';
+import type { Queries, QueryResults, SupportedQueryTypes } from '../../queries/query';
+import { DEFAULT_DATAFLOW_PIPELINE } from '../../core/steps/pipeline/default-pipelines';
 import type { SupportedVirtualQueryTypes } from '../../queries/virtual-query/virtual-queries';
 import type { VirtualCompoundConstraint } from '../../queries/virtual-query/compound-query';
-export interface ShowQueryOptions {
+import type { PipelineOutput } from '../../core/steps/pipeline/pipeline';
+export interface ShowQueryOptions<Base extends SupportedQueryTypes> {
     readonly showCode?: boolean;
     readonly collapseResult?: boolean;
     readonly collapseQuery?: boolean;
+    readonly addOutput?: (result: QueryResults<Base>, pipeline: PipelineOutput<typeof DEFAULT_DATAFLOW_PIPELINE>) => string;
 }
-export declare function showQuery<Base extends SupportedQueryTypes, VirtualArguments extends VirtualCompoundConstraint<Base> = VirtualCompoundConstraint<Base>>(shell: RShell, code: string, queries: Queries<Base, VirtualArguments>, { showCode, collapseResult, collapseQuery }?: ShowQueryOptions): Promise<string>;
+export declare function showQuery<Base extends SupportedQueryTypes, VirtualArguments extends VirtualCompoundConstraint<Base> = VirtualCompoundConstraint<Base>>(shell: RShell, code: string, queries: Queries<Base, VirtualArguments>, { showCode, collapseResult, collapseQuery, addOutput }?: ShowQueryOptions<Base>): Promise<string>;
 export interface QueryDocumentation {
     readonly name: string;
     readonly type: 'virtual' | 'active';

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

@@ -17,7 +17,7 @@ const doc_dfg_1 = require("./doc-dfg");
 const doc_code_1 = require("./doc-code");
 const time_1 = require("../../util/text/time");
 const query_print_1 = require("../../queries/query-print");
-async function showQuery(shell, code, queries, { showCode, collapseResult, collapseQuery } = {}) {
+async function showQuery(shell, code, queries, { showCode, collapseResult, collapseQuery, addOutput = () => '' } = {}) {
     const now = performance.now();
     const analysis = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
         parser: shell,
@@ -60,6 +60,8 @@ ${await (0, doc_dfg_1.printDfGraphForCode)(shell, code, { switchCodeAndGraph: tr
 
 ${collapseResult ? '</details>' : ''}
 
+${addOutput(results, analysis)}
+
 	`;
 }
 exports.RegisteredQueries = {

package/documentation/print-cfg-wiki.js

@@ -89,10 +89,10 @@ class CollectNumbersSyntaxVisitor extends syntax_cfg_guided_visitor_1.SyntaxAwar
 class CollectNumbersDataflowVisitor extends dfg_cfg_guided_visitor_1.DataflowAwareCfgGuidedVisitor {
     numbers = [];
     constructor(controlFlow, dataflow) {
-        super({ controlFlow, dataflow, defaultVisitingOrder: 'forward' });
+        super({ controlFlow, dfg: dataflow, defaultVisitingOrder: 'forward' });
     }
     visitValue(node) {
-        const astNode = this.config.dataflow.graph.idMap?.get(node.id);
+        const astNode = this.config.dfg.idMap?.get(node.id);
         if ((0, r_number_1.isRNumber)(astNode)) {
             this.numbers.push(astNode.content);
         }
@@ -104,7 +104,7 @@ class CollectNumbersDataflowVisitor extends dfg_cfg_guided_visitor_1.DataflowAwa
 class CollectSourcesSemanticVisitor extends semantic_cfg_guided_visitor_1.SemanticCfgGuidedVisitor {
     sources = [];
     constructor(controlFlow, normalizedAst, dataflow) {
-        super({ controlFlow, normalizedAst, dataflow, defaultVisitingOrder: 'forward' });
+        super({ controlFlow, normalizedAst, dfg: dataflow, defaultVisitingOrder: 'forward' });
     }
     onAssignmentCall({ source }) {
         if (source) {
@@ -206,7 +206,7 @@ ${(0, doc_structure_1.section)('Structure of the Control Flow Graph', 2, 'cfg-st
 You can produce your very own control flow graph with ${(0, doc_types_1.shortLink)(extract_cfg_1.extractCfg.name, types.info)}.
 The ${(0, doc_types_1.shortLink)(control_flow_graph_1.ControlFlowGraph.name, types.info)} class describes everything required to model the control flow graph, with its edge types described by
  ${(0, doc_types_1.shortLink)('CfgEdge', types.info)} and its vertices by ${(0, doc_types_1.shortLink)('CfgSimpleVertex', types.info)}.
-However, you should be aware of the ${(0, doc_types_1.shortLink)('ControlFlowInformation', types.info)} interface which adds some additional information the the CFG
+However, you should be aware of the ${(0, doc_types_1.shortLink)('ControlFlowInformation', types.info)} interface which adds some additional information the CFG
 (and is used during the construction of the CFG as well):
 
 ${(0, doc_types_1.printHierarchy)({ info: types.info, root: 'ControlFlowInformation', program: types.program, openTop: true })}
@@ -475,7 +475,7 @@ Again, executing it with the CFG and Dataflow of the expression \`x - 1 + 2L * 3
 
 ${await (async () => {
         const res = await (0, doc_cfg_1.getCfg)(shell, 'x - 1 + 2L * 3');
-        const visitor = new CollectNumbersDataflowVisitor(res.info, res.dataflow);
+        const visitor = new CollectNumbersDataflowVisitor(res.info, res.dataflow.graph);
         visitor.start();
         const collected = visitor.getNumbers();
         return collected.map(n => '\n- `' + JSON.stringify(n) + '`').join('');
@@ -500,7 +500,7 @@ Executing it with the CFG and Dataflow of the expression \`x <- 2; 3 -> x; assig
 
 ${await (async () => {
         const res = await (0, doc_cfg_1.getCfg)(shell, 'x <- 2; 3 -> x; assign("x", 42 + 21)');
-        const visitor = new CollectSourcesSemanticVisitor(res.info, res.ast, res.dataflow);
+        const visitor = new CollectSourcesSemanticVisitor(res.info, res.ast, res.dataflow.graph);
         visitor.start();
         const collected = visitor.getSources();
         return collected.map(n => '\n- `' + n + '`').join('');

package/documentation/print-dataflow-graph-wiki.js

@@ -34,6 +34,7 @@ const linker_1 = require("../dataflow/internal/linker");
 const doc_normalized_ast_1 = require("./doc-util/doc-normalized-ast");
 const dfg_get_origin_1 = require("../dataflow/origin/dfg-get-origin");
 const identify_link_to_last_call_relation_1 = require("../queries/catalog/call-context-query/identify-link-to-last-call-relation");
+const alias_tracking_1 = require("../dataflow/eval/resolve/alias-tracking");
 const doc_issue_1 = require("./doc-util/doc-issue");
 const unnamed_call_handling_1 = require("../dataflow/internal/process/functions/call/unnamed-call-handling");
 const environment_builder_1 = require("../../test/functionality/_helper/dataflow/environment-builder");
@@ -977,7 +978,7 @@ Depending on what you are interested in, there exists a plethora of functions an
 * The **[Query API](${doc_files_1.FlowrWikiBaseRef}/Query%20API)** provides many functions to query the dataflow graph for specific information (dependencies, calls, slices, clusters, ...)
 * The **[Search API](${doc_files_1.FlowrWikiBaseRef}/Search%20API)** allows you to search for specific vertices or edges in the dataflow graph or the original program
 * ${(0, doc_types_1.shortLink)(node_id_1.recoverName.name, vertexType.info)} and ${(0, doc_types_1.shortLink)(node_id_1.recoverContent.name, vertexType.info)} to get the name or content of a vertex in the dataflow graph
-* ${(0, doc_types_1.shortLink)(resolve_by_name_1.resolveValueOfVariable.name, vertexType.info)} and ${(0, doc_types_1.shortLink)(resolve_by_name_1.resolveIdToValue.name, vertexType.info)} to resolve the value of a variable or id (if possible, see [below](#dfg-resolving-values))
+* ${(0, doc_types_1.shortLink)(alias_tracking_1.resolveIdToValue.name, vertexType.info)} to resolve the value of a variable or id (if possible, see [below](#dfg-resolving-values))
 * ${(0, doc_types_1.shortLink)(edge_1.edgeIncludesType.name, vertexType.info)} to check if an edge includes a specific type and ${(0, doc_types_1.shortLink)(edge_1.splitEdgeTypes.name, vertexType.info)} to split the bitmask of edges into its types (see [below](#dfg-resolving-values))
 * ${(0, doc_types_1.shortLink)(identify_link_to_last_call_relation_1.getValueOfArgument.name, vertexType.info)} to get the (syntactical) value of an argument in a function call 
 * ${(0, doc_types_1.shortLink)(dfg_get_origin_1.getOriginInDfg.name, vertexType.info)} to get information about where a read, call, ... comes from (see [below](#dfg-resolving-values))
@@ -989,8 +990,8 @@ ${(0, doc_structure_1.section)('Resolving Values', 3, 'dfg-resolving-values')}
 FlowR supports a [configurable](${doc_files_1.FlowrWikiBaseRef}/Interface#configuring-flowr) level of value tracking—all with the goal of knowing the static value domain of a variable.
 These capabilities are exposed by the [resolve value Query](${doc_files_1.FlowrWikiBaseRef}/Query-API#resolve-value-query) and backed by two important functions:
 
-${(0, doc_types_1.shortLink)(resolve_by_name_1.resolveValueOfVariable.name, vertexType.info)} provides an environment-sensitive (see ${(0, doc_types_1.shortLink)('REnvironmentInformation', vertexType.info)})
-value resolution, while ${(0, doc_types_1.shortLink)(resolve_by_name_1.resolveIdToValue.name, vertexType.info)} provides a more general, but potentially less precise resolution independent of the current state.
+${(0, doc_types_1.shortLink)(alias_tracking_1.resolveIdToValue.name, vertexType.info)} provides an environment-sensitive (see ${(0, doc_types_1.shortLink)('REnvironmentInformation', vertexType.info)})
+value resolution depending on if the environment is provided.
 
 ${(0, doc_structure_1.section)('Assessing Edges', 3, 'dfg-assess-edge')}
 

package/documentation/print-engines-wiki.js

@@ -49,7 +49,7 @@ are exposed with some command line options (e.g., when using the docker image of
 
 ${(0, doc_structure_1.block)({
         type: 'WARNING',
-        content: 'As the tree-sitter engine is only for parsing, it cannot execute R code.'
+        content: 'As the tree-sitter engine is only for parsing, it cannot execute R code. This engine is now the default.'
     })}
 
 In general, there is no need for you to pass custom paths using either 

package/documentation/print-query-wiki.js

@@ -34,6 +34,8 @@ const flowr_search_builder_1 = require("../search/flowr-search-builder");
 const vertex_1 = require("../dataflow/graph/vertex");
 const doc_types_1 = require("./doc-util/doc-types");
 const path_1 = __importDefault(require("path"));
+const control_flow_query_executor_1 = require("../queries/catalog/control-flow-query/control-flow-query-executor");
+const doc_cfg_1 = require("./doc-util/doc-cfg");
 (0, doc_query_1.registerQueryDocumentation)('call-context', {
     name: 'Call-Context Query',
     type: 'active',
@@ -477,6 +479,84 @@ Here, \`resolveValue\` tells the dependency query to resolve the value of this a
 		`;
     }
 });
+(0, doc_query_1.registerQueryDocumentation)('linter', {
+    name: 'Linter Query',
+    type: 'active',
+    shortDescription: 'Lints a given R script for common issues.',
+    functionName: dependencies_query_executor_1.executeDependenciesQuery.name,
+    functionFile: '../queries/catalog/linter-query/linter-query-executor.ts',
+    buildExplanation: async (shell) => {
+        const exampleCode = 'read.csv("i_do_not_exist.csv")';
+        return `
+This query lints a given R script for common issues, such as missing files, unused variables, and more.
+
+In other words, if you have a script simply reading: \`${exampleCode}\`, the following query returns all smells detected:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'linter'
+            }], { showCode: false, collapseQuery: true })}
+
+You can also configure which rules to apply and what settings to use for these rules. 
+We welcome any feedback and suggestions for new rules on this (consider opening a [new issue](${doc_issue_1.NewIssueUrl})).
+		`;
+    }
+});
+(0, doc_query_1.registerQueryDocumentation)('control-flow', {
+    name: 'Control-Flow Query',
+    type: 'active',
+    shortDescription: 'Provides the control-flow of the program.',
+    functionName: control_flow_query_executor_1.executeControlFlowQuery.name,
+    functionFile: '../queries/catalog/control-flow-query/control-flow-query-executor.ts',
+    buildExplanation: async (shell) => {
+        const exampleCode = 'if(TRUE) 1 else 2';
+        return `
+This control-flow query provides you access to the control flow graph.
+
+In other words, if you have a script simply reading: \`${exampleCode}\`, the following query returns the CFG:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'control-flow'
+            }], { showCode: false, collapseQuery: true, collapseResult: true })}
+
+You can also overwrite the simplification passes to tune the perspective. for example, if you want to have basic blocks:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'control-flow',
+                config: {
+                    simplificationPasses: ['unique-cf-sets', 'to-basic-blocks']
+                }
+            }], { showCode: false, collapseResult: true })}
+
+this produces: 
+
+${await (0, doc_cfg_1.printCfgCode)(shell, exampleCode, { showCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'] })}
+
+
+If, on the other hand, you want to prune dead code edges:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'control-flow',
+                config: {
+                    simplificationPasses: ['unique-cf-sets', 'analyze-dead-code']
+                }
+            }], { showCode: false, collapseResult: true })}
+
+this produces:
+
+${await (0, doc_cfg_1.printCfgCode)(shell, exampleCode, { showCode: false, prefix: 'flowchart RL\n', simplifications: ['analyze-dead-code'] })}
+
+
+Or, completely remove dead code:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'control-flow',
+                config: {
+                    simplificationPasses: ['unique-cf-sets', 'analyze-dead-code', 'remove-dead-code']
+                }
+            }], { showCode: false, collapseResult: true })}
+
+this produces:
+
+${await (0, doc_cfg_1.printCfgCode)(shell, exampleCode, { showCode: false, prefix: 'flowchart RL\n', simplifications: ['analyze-dead-code', 'remove-dead-code'] })}
+
+		`;
+    }
+});
 (0, doc_query_1.registerQueryDocumentation)('location-map', {
     name: 'Location Map Query',
     type: 'active',

package/linter/rules/1-deprecated-functions.js

@@ -46,7 +46,7 @@ exports.R1_DEPRECATED_FUNCTIONS = {
             '.meta': metadata
         };
     },
-    prettyPrint: result => `Function ${result.function} at ${(0, dfg_1.formatRange)(result.range)}`,
+    prettyPrint: result => `Function \`${result.function}\` at ${(0, dfg_1.formatRange)(result.range)}`,
     defaultConfig: {
         deprecatedFunctions: ['all_equal', 'arrange_all', 'distinct_all', 'filter_all', 'group_by_all', 'summarise_all', 'mutate_all', 'select_all', 'vars', 'all_vars', 'id', 'failwith', 'select_vars', 'rename_vars', 'select_var', 'current_vars', 'bench_tbls', 'compare_tbls', 'compare_tbls2', 'eval_tbls', 'eval_tbls2', 'location', 'changes', 'combine', 'do', 'funs', 'add_count_', 'add_tally_', 'arrange_', 'count_', 'distinct_', 'do_', 'filter_', 'funs_', 'group_by_', 'group_indices_', 'mutate_', 'tally_', 'transmute_', 'rename_', 'rename_vars_', 'select_', 'select_vars_', 'slice_', 'summarise_', 'summarize_', 'summarise_each', 'src_local', 'tbl_df', 'add_rownames', 'group_nest', 'group_split', 'with_groups', 'nest_by', 'progress_estimated', 'recode', 'sample_n', 'top_n', 'transmute', 'fct_explicit_na', 'aes_', 'aes_auto', 'annotation_logticks', 'is.Coord', 'coord_flip', 'coord_map', 'is.facet', 'fortify', 'is.ggproto', 'guide_train', 'is.ggplot', 'qplot', 'is.theme', 'gg_dep', 'liply', 'isplit2', 'list_along', 'cross', 'invoke', 'at_depth', 'prepend', 'rerun', 'splice', '`%@%`', 'rbernoulli', 'rdunif', 'when', 'update_list', 'map_raw', 'accumulate', 'reduce_right', 'flatten', 'map_dfr', 'as_vector', 'transpose', 'melt_delim', 'melt_fwf', 'melt_table', 'read_table2', 'str_interp', 'as_tibble', 'data_frame', 'tibble_', 'data_frame_', 'lst_', 'as_data_frame', 'as.tibble', 'frame_data', 'trunc_mat', 'is.tibble', 'tidy_names', 'set_tidy_names', 'repair_names', 'extract_numeric', 'complete_', 'drop_na_', 'expand_', 'crossing_', 'nesting_', 'extract_', 'fill_', 'gather_', 'nest_', 'separate_rows_', 'separate_', 'spread_', 'unite_', 'unnest_', 'extract', 'gather', 'nest_legacy', 'separate_rows', 'separate', 'spread',]
     }

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

@@ -76,7 +76,7 @@ exports.R2_FILE_PATH_VALIDITY = {
             '.meta': metadata
         };
     },
-    prettyPrint: result => `Path ${result.filePath} at ${(0, dfg_1.formatRange)(result.range)}`,
+    prettyPrint: result => `Path \`${result.filePath}\` at ${(0, dfg_1.formatRange)(result.range)}`,
     defaultConfig: {
         additionalReadFunctions: [],
         additionalWriteFunctions: [],