@eagleoutice/flowr 2.2.13 → 2.2.15

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-cfg.d.ts

@@ -19,5 +19,5 @@ export interface PrintCfgOptions {
     readonly simplify?: boolean;
     readonly useDfg?: boolean;
 }
-export declare function printCFGCode(parser: KnownParser, code: string, { showCode, openCode, prefix, simplifications, simplify, useDfg }?: PrintCfgOptions): Promise<string>;
+export declare function printCfgCode(parser: KnownParser, code: string, { showCode, openCode, prefix, simplifications, simplify, useDfg }?: PrintCfgOptions): Promise<string>;
 export {};

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

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getCfg = getCfg;
 exports.printCfg = printCfg;
-exports.printCFGCode = printCFGCode;
+exports.printCfgCode = printCfgCode;
 const extract_cfg_1 = require("../../control-flow/extract-cfg");
 const default_pipelines_1 = require("../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../r-bridge/retriever");
@@ -17,7 +17,7 @@ async function getCfg(parser, code, simplifications = [], useDfg = true) {
     }).allRemainingSteps() : await (0, default_pipelines_1.createNormalizePipeline)(parser, {
         request: (0, retriever_1.requestFromInput)(code)
     }).allRemainingSteps();
-    const cfg = (0, extract_cfg_1.extractCFG)(result.normalize, useDfg ? result.dataflow.graph : undefined, [...cfg_simplification_1.DefaultCfgSimplificationOrder, ...simplifications]);
+    const cfg = (0, extract_cfg_1.extractCfg)(result.normalize, useDfg ? result.dataflow.graph : undefined, [...cfg_simplification_1.DefaultCfgSimplificationOrder, ...simplifications]);
     return {
         info: cfg,
         ast: result.normalize,
@@ -29,7 +29,7 @@ function printCfg(cfg, ast, prefix = 'flowchart BT\n', simplify = false) {
 ${(0, doc_code_1.codeBlock)('mermaid', (0, cfg_1.cfgToMermaid)(cfg, ast, prefix, simplify))}
 	`;
 }
-async function printCFGCode(parser, code, { showCode = true, openCode = false, prefix = 'flowchart BT\n', simplifications = [], simplify = false, useDfg = true } = {}) {
+async function printCfgCode(parser, code, { showCode = true, openCode = false, prefix = 'flowchart BT\n', simplifications = [], simplify = false, useDfg = true } = {}) {
     const now = performance.now();
     const res = await getCfg(parser, code, simplifications, useDfg);
     const duration = performance.now() - now;

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) {
@@ -167,7 +167,7 @@ ${(0, doc_code_1.codeBlock)('r', 'x <- 2 * 3 + 1')}
 
 The corresponding CFG is a directed, labeled graph with two types of edges (control and flow dependencies).
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'x <- 2 * 3 + 1', { showCode: false, prefix: 'flowchart RL\n' })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'x <- 2 * 3 + 1', { showCode: false, prefix: 'flowchart RL\n' })}
 
 ${(0, doc_structure_1.block)({
         type: 'IMPORTANT',
@@ -180,33 +180,33 @@ Expressions, such as \`2 * 3\` get an additional node with an artificial id that
 
 To gain a better understanding, let's have a look at a simple program with a single branching structure:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'if(u) 3 else 2', { showCode: true, openCode: false, prefix: 'flowchart RL\n' })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'if(u) 3 else 2', { showCode: true, openCode: false, prefix: 'flowchart RL\n' })}
 
 Here, you can see the \`if\` node followed by the condition (in this case merely \`u\`) that then splits into two branches for the two possible outcomes.
 The \`if\` structure is terminated by the corresponding \`-exit\` node (see the [structure](#cfg-structure) section for more details).
 
 For you to compare, the following shows the CFG of an \`if\` without an \`else\` branch:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'if(u || v) 3', { showCode: true, openCode: false, prefix: 'flowchart RL\n' })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'if(u || v) 3', { showCode: true, openCode: false, prefix: 'flowchart RL\n' })}
 
 Activating the calculation of basic blocks produces the following:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'if(u || v) 3', { showCode: true, openCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'] })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'if(u || v) 3', { showCode: true, openCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'] })}
 
 Which is probably much more readable if compacted (although the reconstucted code can sometimes be slightly mislieading as flowR tries its best to make it syntactically correct and hence add closing braces etc. which are technically not part of the respective block):
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'if(u || v) 3', { showCode: true, openCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'], simplify: true })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'if(u || v) 3', { showCode: true, openCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'], simplify: true })}
 
 The control flow graph also harmonizes with function definitions, and calls:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'f <- function() { 3 }\nf()', { showCode: true, openCode: true, prefix: 'flowchart RL\n' })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'f <- function() { 3 }\nf()', { showCode: true, openCode: true, prefix: 'flowchart RL\n' })}
 
 ${(0, doc_structure_1.section)('Structure of the Control Flow Graph', 2, 'cfg-structure')}
 
-You can produce your very own control flow graph with ${(0, doc_types_1.shortLink)(extract_cfg_1.extractCFG.name, types.info)}.
+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 })}
@@ -214,7 +214,7 @@ ${(0, doc_types_1.printHierarchy)({ info: types.info, root: 'ControlFlowInformat
 To check whether the CFG has the expected shape, you can use the test function ${(0, doc_types_1.shortLink)('assertCfg', testTypes.info)} which supports testing for
  sub-graphs as well (it provides diffing capabilities similar to ${(0, doc_types_1.shortLink)('assertDataflow', testTypes.info)}).
 As the CFG may become unhandy for larger programs, there are simplifications available with ${(0, doc_types_1.shortLink)(cfg_simplification_1.simplifyControlFlowInformation.name, types.info)}
-(these can be passed on to the ${(0, doc_types_1.shortLink)(extract_cfg_1.extractCFG.name, types.info)} function as well).
+(these can be passed on to the ${(0, doc_types_1.shortLink)(extract_cfg_1.extractCfg.name, types.info)} function as well).
 
 ${(0, doc_structure_1.section)('CFG Vertices', 3, 'cfg-structure-vertices')}
 
@@ -258,7 +258,7 @@ ${(0, doc_structure_1.section)('Flow Dependencies', 4, 'cfg-flow-dependency')}
 The most common edge is the flow dependency&nbsp;(FD) which simply signals that the source vertex happens _after_ the target vertex in the control flow.
 So \`x; y\` would produce a flow dependency from \`y\` to \`x\` (additionally to the program-enveloping root expression list):
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'x; y', { showCode: false, prefix: 'flowchart RL\n' })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'x; y', { showCode: false, prefix: 'flowchart RL\n' })}
 
 ${(0, doc_structure_1.section)('Control Dependencies', 4, 'cfg-control-dependency')}
 
@@ -271,12 +271,12 @@ The extra \`caused\` link signals the vertex that caused the control flow influe
 
 
 ${await (async () => {
-        const exa = await (0, doc_cfg_1.printCFGCode)(shell, 'if(u) 3 else 2', { showCode: true, prefix: 'flowchart RL\n' });
+        const exa = await (0, doc_cfg_1.printCfgCode)(shell, 'if(u) 3 else 2', { showCode: true, prefix: 'flowchart RL\n' });
         return (0, doc_structure_1.details)('Example: if-else', exa);
     })()}
 
 ${await (async () => {
-        const exa = await (0, doc_cfg_1.printCFGCode)(shell, 'while(u) b', { showCode: true, prefix: 'flowchart RL\n' });
+        const exa = await (0, doc_cfg_1.printCfgCode)(shell, 'while(u) b', { showCode: true, prefix: 'flowchart RL\n' });
         return (0, doc_structure_1.details)('Example: while-loop', exa);
     })()}
 <br/>
@@ -286,12 +286,12 @@ Additionally, the control flow graph does not have to be connected. If you use a
 the corresponding exit markers are not reachable from the entry:
 
 ${await (async () => {
-        const exa = await (0, doc_cfg_1.printCFGCode)(shell, 'repeat { b }; after', { showCode: true, prefix: 'flowchart RL\n' });
+        const exa = await (0, doc_cfg_1.printCfgCode)(shell, 'repeat { b }; after', { showCode: true, prefix: 'flowchart RL\n' });
         return (0, doc_structure_1.details)('Example: repeat-loop (infinite)', exa);
     })()}
 
 ${await (async () => {
-        const exa = await (0, doc_cfg_1.printCFGCode)(shell, 'repeat { b; if(u) break; }; after', { showCode: true, prefix: 'flowchart RL\n' });
+        const exa = await (0, doc_cfg_1.printCfgCode)(shell, 'repeat { b; if(u) break; }; after', { showCode: true, prefix: 'flowchart RL\n' });
         return (0, doc_structure_1.details)('Example: repeat-loop (with break)', exa);
     })()}
 <br/>
@@ -299,22 +299,22 @@ ${await (async () => {
 In the context of a for-loop, the control dependency refer to whether the respective vector still has values to iterate over.
 
 ${await (async () => {
-        const exa = await (0, doc_cfg_1.printCFGCode)(shell, 'for(i in 1:10) b', { showCode: true, prefix: 'flowchart RL\n' });
+        const exa = await (0, doc_cfg_1.printCfgCode)(shell, 'for(i in 1:10) b', { showCode: true, prefix: 'flowchart RL\n' });
         return (0, doc_structure_1.details)('Example: for-loop', exa);
     })()}
 
 ${(0, doc_structure_1.section)('Extra: Call Links', 4, 'cfg-call-links')}
 
-If you generate the CFG with the ${(0, doc_types_1.shortLink)(extract_cfg_1.extractCFG.name, types.info)} function you can (and, if you want to gain inter-procedural information, should)
+If you generate the CFG with the ${(0, doc_types_1.shortLink)(extract_cfg_1.extractCfg.name, types.info)} function you can (and, if you want to gain inter-procedural information, should)
 pass a matching [dataflow graph](${doc_files_1.FlowrWikiBaseRef}/Dataflow%20Graph) to it to incorporate the dataflow perspective into the CFG.
 
 The difference becomes obvious when we look at the code \`f <- function() b; f()\` first without the dataflow graph:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'f <- function() b; f()', { showCode: true, prefix: 'flowchart RL\n', useDfg: false })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'f <- function() b; f()', { showCode: true, prefix: 'flowchart RL\n', useDfg: false })}
 
 And now, including dataflow information:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'f <- function() b; f()', { showCode: true, prefix: 'flowchart RL\n', useDfg: true })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'f <- function() b; f()', { showCode: true, prefix: 'flowchart RL\n', useDfg: true })}
 
 There are two important additions:
 
@@ -325,7 +325,7 @@ There are two important additions:
 For built-in functions that are provided by flowR's built-in configuration (see the [interface wiki page](${doc_files_1.FlowrWikiBaseRef}/Interface)) the CFG does not contain
 the additional information directly:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'print(3)', { showCode: true, prefix: 'flowchart RL\n' })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'print(3)', { showCode: true, prefix: 'flowchart RL\n' })}
 
 This is due to the fact that the [dataflow graph](${doc_files_1.FlowrWikiBaseRef}/Dataflow%20Graph) does contain the required call information (and there are no new control vertices to add as the built-in call has no target in the source code):
 
@@ -340,16 +340,16 @@ Yet, we can request basic blocks or transform an existing CFG into basic blocks
 
 Any program without any (un-)conditional jumps now contains a single basic block:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'x <- 2 * 3 + 1', { showCode: true, openCode: true, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'], simplify: true })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'x <- 2 * 3 + 1', { showCode: true, openCode: true, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'], simplify: true })}
 
 While the CFG without basic blocks is much bigger:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'x <- 2 * 3 + 1', { showCode: false, prefix: 'flowchart RL\n' })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'x <- 2 * 3 + 1', { showCode: false, prefix: 'flowchart RL\n' })}
 
 In a way, using the basic blocks perspective does not remove any of these vertices (we just usually visualize them compacted as their execution order should be "obvious").
 The vertices are still there, as elems of the ${(0, doc_types_1.shortLink)('CfgBasicBlockVertex', types.info)}:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, 'x <- 2 * 3 + 1', { showCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'], simplify: false })}
+${await (0, doc_cfg_1.printCfgCode)(shell, 'x <- 2 * 3 + 1', { showCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'], simplify: false })}
 
 The benefit (for comprehensibility and algorithms) becomes more apparent when we look at a more complicated program:
 
@@ -357,12 +357,12 @@ ${(0, doc_code_1.codeBlock)('r', CfgLongExample)}
 
 With basic blocks, this code looks like this:
 
-${await (0, doc_cfg_1.printCFGCode)(shell, CfgLongExample, { showCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'], simplify: true })}
+${await (0, doc_cfg_1.printCfgCode)(shell, CfgLongExample, { showCode: false, prefix: 'flowchart RL\n', simplifications: ['to-basic-blocks'], simplify: true })}
 
 Now, without basic blocks, this is a different story...
 
 ${await (async () => {
-        const exa = await (0, doc_cfg_1.printCFGCode)(shell, CfgLongExample, { showCode: false, prefix: 'flowchart RL\n' });
+        const exa = await (0, doc_cfg_1.printCfgCode)(shell, CfgLongExample, { showCode: false, prefix: 'flowchart RL\n' });
         return (0, doc_structure_1.details)('The full CFG', exa);
     })()}
 
@@ -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('');
@@ -529,7 +529,7 @@ ${await (async function () {
         (0, assert_1.guard)(plusVertex.type === control_flow_graph_1.CfgVertexType.Expression);
         const numOfExits = plusVertex.end?.length ?? 0;
         (0, assert_1.guard)(plusVertex.end && numOfExits === 1);
-        return `${await (0, doc_cfg_1.printCFGCode)(shell, 'x + 1', { showCode: true, prefix: 'flowchart RL\n' })}
+        return `${await (0, doc_cfg_1.printCfgCode)(shell, 'x + 1', { showCode: true, prefix: 'flowchart RL\n' })}
 	
 Looking at the binary operation vertex for \`+\` (with id \`${plusVertexId}\`) we see that it is linked to a single exit ("end marker") point: \`${plusVertex.end[0]}\`.
 Checking this vertex essentially reveals all exit points of the expression &dash; in this case, this simply refers to the operands of the addition.
@@ -544,7 +544,7 @@ ${(0, doc_structure_1.details)('Example: Exit Points for an if', await (async fu
         (0, assert_1.guard)(ifVertex.type === control_flow_graph_1.CfgVertexType.Statement);
         const numOfExits = ifVertex.end?.length ?? 0;
         (0, assert_1.guard)(ifVertex.end && numOfExits === 1);
-        return `${await (0, doc_cfg_1.printCFGCode)(shell, expr, { showCode: true, prefix: 'flowchart RL\n' })}
+        return `${await (0, doc_cfg_1.printCfgCode)(shell, expr, { showCode: true, prefix: 'flowchart RL\n' })}
 	
 Looking at the if vertex for (with id \`${ifVertexId}\`) we see that it is again linked to a single exit point: \`${ifVertex.end[0]}\`.
 Yet, now this exit vertex is linked to the two branches of the if statement (the \`then\` and \`else\` branch).

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-linter-wiki.d.ts

@@ -0,0 +1 @@
+export {};

package/documentation/print-linter-wiki.js

@@ -0,0 +1,76 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const log_1 = require("../../test/functionality/_helper/log");
+const doc_auto_gen_1 = require("./doc-util/doc-auto-gen");
+const doc_files_1 = require("./doc-util/doc-files");
+const linter_rules_1 = require("../linter/linter-rules");
+const doc_code_1 = require("./doc-util/doc-code");
+const shell_1 = require("../r-bridge/shell");
+const doc_query_1 = require("./doc-util/doc-query");
+const doc_types_1 = require("./doc-util/doc-types");
+const path_1 = __importDefault(require("path"));
+async function getText(shell) {
+    const rVersion = (await shell.usedRVersion())?.format() ?? 'unknown';
+    return `${(0, doc_auto_gen_1.autoGenHeader)({ filename: module.filename, purpose: 'linter', rVersion })}
+
+This page describes the flowR linter, which is a tool that utilizes flowR's dataflow analysis to find common issues in R scripts. The linter can currently be used through the linter [query](${doc_files_1.FlowrWikiBaseRef}/Query%20API).
+
+## Linting Rules
+
+The following linting rules are available:
+
+${await rule(shell, 'deprecated-functions', 'DeprecatedFunctionsConfig', 'Deprecated Functions', 'This rule detects the usage of deprecated functions in code based on a predefined list of known deprecated functions.', `
+first <- data.frame(x = c(1, 2, 3), y = c(1, 2, 3))
+second <- data.frame(x = c(1, 3, 2), y = c(1, 3, 2))
+dplyr::all_equal(first, second)
+`)}
+
+${await rule(shell, 'file-path-validity', 'FilePathValidityConfig', 'File Path Validity', 'This rule finds places in the code where files are being read from. In such places, it checks whether the file path is valid and whether the file exists on disk.', `
+my_data <- read.csv("C:/Users/me/Documents/My R Scripts/Reproducible.csv")
+`)}
+
+    `.trim();
+}
+async function rule(shell, name, configType, friendlyName, description, example) {
+    const types = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+        rootFolder: path_1.default.resolve('./src/linter/'),
+        typeName: configType,
+        inlineTypes: doc_types_1.mermaidHide
+    });
+    return `
+### ${friendlyName} (\`${name}\`)
+	
+${description}
+
+<details>
+
+#### Configuration
+
+Linting rules can be configured by passing a configuration object to the linter query as shown in the example below. The \`${name}\` rule accepts the following configuration options:
+
+${Object.getOwnPropertyNames(linter_rules_1.LintingRules[name].defaultConfig).sort().map(key => `- ${(0, doc_types_1.shortLink)(`${configType}:::${key}`, types.info)}\\\n${(0, doc_types_1.getDocumentationForType)(`${configType}::${key}`, types.info)}`).join('\n')}
+
+#### Example
+
+${(0, doc_code_1.codeBlock)('r', example)}
+
+The linting query can be used to run this rule on the above example:
+
+${await (0, doc_query_1.showQuery)(shell, example, [{ type: 'linter', rules: [{ name, config: {} }] }], { collapseQuery: true })}
+
+</details>
+	`.trim();
+}
+if (require.main === module) {
+    (0, log_1.setMinLevelOfAllLogs)(6 /* LogLevel.Fatal */);
+    const shell = new shell_1.RShell();
+    void getText(shell).then(str => {
+        console.log(str);
+    }).finally(() => {
+        shell.close();
+    });
+}
+//# sourceMappingURL=print-linter-wiki.js.map