@eagleoutice/flowr 2.1.2 → 2.1.4

package/benchmark/slicer.js

@@ -64,7 +64,7 @@ class BenchmarkSlicer {
             criterion: [],
             autoSelectIf
         });
-        this.loadedXml = await this.measureCommonStep('parse', 'retrieve AST from R code');
+        this.loadedXml = (await this.measureCommonStep('parse', 'retrieve AST from R code')).parsed;
         this.normalizedAst = await this.measureCommonStep('normalize', 'normalize R AST');
         this.dataflow = await this.measureCommonStep('dataflow', 'produce dataflow information');
         this.pipeline.switchToRequestStage();

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

@@ -95,7 +95,7 @@ exports.parseCommand = {
             shell,
             request: (0, retriever_1.requestFromInput)((0, retriever_1.removeRQuotes)(remainingLine.trim()))
         }).allRemainingSteps();
-        const object = (0, format_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(result.parse));
+        const object = (0, format_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(result.parse.parsed));
         output.stdout(depthListToTextTree(toDepthMap(object), output.formatter));
     }
 };

package/cli/repl/commands/repl-query.d.ts

@@ -1,8 +1,3 @@
-import { DEFAULT_DATAFLOW_PIPELINE } from '../../../core/steps/pipeline/default-pipelines';
 import type { ReplCommand } from './repl-main';
-import type { OutputFormatter } from '../../../util/ansi';
-import type { QueryResults, SupportedQueryTypes } from '../../../queries/query';
-import type { PipelineOutput } from '../../../core/steps/pipeline/pipeline';
-export declare function asciiSummaryOfQueryResult(formatter: OutputFormatter, totalInMs: number, results: QueryResults<SupportedQueryTypes>, processed: PipelineOutput<typeof DEFAULT_DATAFLOW_PIPELINE>): string;
 export declare const queryCommand: ReplCommand;
 export declare const queryStarCommand: ReplCommand;

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

@@ -1,7 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.queryStarCommand = exports.queryCommand = void 0;
-exports.asciiSummaryOfQueryResult = asciiSummaryOfQueryResult;
 const pipeline_executor_1 = require("../../../core/pipeline-executor");
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../../r-bridge/retriever");
@@ -10,12 +9,7 @@ const ansi_1 = require("../../../util/ansi");
 const schema_1 = require("../../../util/schema");
 const query_1 = require("../../../queries/query");
 const json_1 = require("../../../util/json");
-const query_schema_1 = require("../../../queries/query-schema");
-const built_in_1 = require("../../../dataflow/environments/built-in");
-const dfg_1 = require("../../../util/mermaid/dfg");
-const ast_1 = require("../../../util/mermaid/ast");
-const time_1 = require("../../../util/time");
-const doc_hover_over_1 = require("../../../documentation/doc-util/doc-hover-over");
+const query_print_1 = require("../../../queries/query-print");
 async function getDataflow(shell, remainingLine) {
     return await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
         shell,
@@ -25,7 +19,7 @@ async function getDataflow(shell, remainingLine) {
 function printHelp(output) {
     output.stderr(`Format: ${(0, ansi_1.italic)(':query "<query>" <code>', output.formatter)}`);
     output.stdout('The query is an array of query objects to represent multiple queries. Each query object may have the following properties:');
-    output.stdout((0, schema_1.describeSchema)(query_schema_1.AnyQuerySchema, output.formatter));
+    output.stdout((0, schema_1.describeSchema)(query_1.AnyQuerySchema, output.formatter));
     output.stdout(`\n\nThe example ${(0, ansi_1.italic)(':query "[{\\"type\\": \\"call-context\\", \\"callName\\": \\"mean\\" }]" mean(1:10)', output.formatter)} would return the call context of the mean function.`);
     output.stdout('As a convenience, we interpret any (non-help) string not starting with \'[\' as a regex for the simple call-context query.');
     output.stdout(`Hence, ${(0, ansi_1.italic)(':query "mean" mean(1:10)', output.formatter)} is equivalent to the above example.`);
@@ -44,7 +38,7 @@ async function processQueryArgs(line, shell, output) {
     let parsedQuery = [];
     if (query.startsWith('[')) {
         parsedQuery = JSON.parse(query);
-        const validationResult = query_schema_1.QueriesSchema.validate(parsedQuery);
+        const validationResult = query_1.QueriesSchema.validate(parsedQuery);
         if (validationResult.error) {
             output.stderr(`Invalid query: ${validationResult.error.message}`);
             printHelp(output);
@@ -60,141 +54,6 @@ async function processQueryArgs(line, shell, output) {
         processed
     };
 }
-function nodeString(id, formatter, processed) {
-    if (id === built_in_1.BuiltIn) {
-        return (0, ansi_1.italic)('built-in', formatter);
-    }
-    const node = processed.normalize.idMap.get(id);
-    if (node === undefined) {
-        return `UNKNOWN: ${id}`;
-    }
-    return `${(0, ansi_1.italic)('`' + (node.lexeme ?? node.info.fullLexeme ?? 'UNKNOWN') + '`', formatter)} (L.${node.location?.[0]})`;
-}
-function asciiCallContextSubHit(formatter, results, processed) {
-    const result = [];
-    for (const { id, calls = [], linkedIds = [], aliasRoots = [] } of results) {
-        const node = processed.normalize.idMap.get(id);
-        if (node === undefined) {
-            result.push(` ${(0, ansi_1.bold)('UNKNOWN: ' + JSON.stringify({ calls, linkedIds }))}`);
-            continue;
-        }
-        let line = nodeString(id, formatter, processed);
-        if (calls.length > 0) {
-            line += ` with ${calls.length} call${calls.length > 1 ? 's' : ''} (${calls.map(c => nodeString(c, formatter, processed)).join(', ')})`;
-        }
-        if (linkedIds.length > 0) {
-            line += ` with ${linkedIds.length} link${linkedIds.length > 1 ? 's' : ''} (${linkedIds.map(c => nodeString(c, formatter, processed)).join(', ')})`;
-        }
-        if (aliasRoots.length > 0) {
-            line += ` with ${aliasRoots.length} alias root${aliasRoots.length > 1 ? 's' : ''} (${aliasRoots.map(c => nodeString(c, formatter, processed)).join(', ')})`;
-        }
-        result.push(line);
-    }
-    return result.join(', ');
-}
-function asciiCallContext(formatter, results, processed) {
-    /* traverse over 'kinds' and within them 'subkinds' */
-    const result = [];
-    for (const [kind, { subkinds }] of Object.entries(results['kinds'])) {
-        result.push(`   ╰ ${(0, ansi_1.bold)(kind, formatter)}`);
-        for (const [subkind, values] of Object.entries(subkinds)) {
-            result.push(`     ╰ ${(0, ansi_1.bold)(subkind, formatter)}: ${asciiCallContextSubHit(formatter, values, processed)}`);
-        }
-    }
-    return result.join('\n');
-}
-function summarizeIdsIfTooLong(ids) {
-    const naive = ids.join(', ');
-    if (naive.length <= 20) {
-        return naive;
-    }
-    let acc = '';
-    let i = 0;
-    while (acc.length <= 20) {
-        acc += ids[i++] + ', ';
-    }
-    if (i < ids.length) {
-        acc += '... (see JSON below)';
-    }
-    return (0, doc_hover_over_1.textWithTooltip)(acc, JSON.stringify(ids));
-}
-function asciiSummaryOfQueryResult(formatter, totalInMs, results, processed) {
-    const result = [];
-    for (const [query, queryResults] of Object.entries(results)) {
-        if (query === '.meta') {
-            continue;
-        }
-        if (query === 'call-context') {
-            const out = queryResults;
-            result.push(`Query: ${(0, ansi_1.bold)(query, formatter)} (${(0, time_1.printAsMs)(out['.meta'].timing, 0)})`);
-            result.push(asciiCallContext(formatter, out, processed));
-            continue;
-        }
-        else if (query === 'dataflow') {
-            const out = queryResults;
-            result.push(`Query: ${(0, ansi_1.bold)(query, formatter)} (${(0, time_1.printAsMs)(out['.meta'].timing, 0)})`);
-            result.push(`   ╰ [Dataflow Graph](${(0, dfg_1.graphToMermaidUrl)(out.graph)})`);
-            continue;
-        }
-        else if (query === 'id-map') {
-            const out = queryResults;
-            result.push(`Query: ${(0, ansi_1.bold)(query, formatter)} (${(0, time_1.printAsMs)(out['.meta'].timing, 0)})`);
-            result.push(`   ╰ Id List: {${summarizeIdsIfTooLong([...out.idMap.keys()])}}`);
-            continue;
-        }
-        else if (query === 'normalized-ast') {
-            const out = queryResults;
-            result.push(`Query: ${(0, ansi_1.bold)(query, formatter)} (${(0, time_1.printAsMs)(out['.meta'].timing, 0)})`);
-            result.push(`   ╰ [Normalized AST](${(0, ast_1.normalizedAstToMermaidUrl)(out.normalized.ast)})`);
-            continue;
-        }
-        else if (query === 'static-slice') {
-            const out = queryResults;
-            result.push(`Query: ${(0, ansi_1.bold)(query, formatter)} (${(0, time_1.printAsMs)(out['.meta'].timing, 0)})`);
-            for (const [fingerprint, obj] of Object.entries(out.results)) {
-                const { criteria, noMagicComments, noReconstruction } = JSON.parse(fingerprint);
-                const addons = [];
-                if (noReconstruction) {
-                    addons.push('no reconstruction');
-                }
-                if (noMagicComments) {
-                    addons.push('no magic comments');
-                }
-                result.push(`   ╰ Slice for {${criteria.join(', ')}} ${addons.join(', ')}`);
-                if ('reconstruct' in obj) {
-                    result.push('     ╰ Code (newline as <code>&#92;n</code>): <code>' + obj.reconstruct.code.split('\n').join('\\n') + '</code>');
-                }
-                else {
-                    result.push(`     ╰ Id List: {${summarizeIdsIfTooLong([...obj.slice.result])}}`);
-                }
-            }
-            continue;
-        }
-        else if (query === 'dataflow-cluster') {
-            const out = queryResults;
-            result.push(`Query: ${(0, ansi_1.bold)(query, formatter)} (${out['.meta'].timing.toFixed(0)}ms)`);
-            result.push(`   ╰ Found ${out.clusters.length} cluster${out.clusters.length === 1 ? '' : 's'}`);
-            for (const cluster of out.clusters) {
-                const unknownSideEffects = cluster.hasUnknownSideEffects ? '(has unknown side effect)' : '';
-                result.push(`      ╰ ${unknownSideEffects} {${summarizeIdsIfTooLong(cluster.members)}} ([marked](${(0, dfg_1.graphToMermaidUrl)(processed.dataflow.graph, false, new Set(cluster.members))}))`);
-            }
-            continue;
-        }
-        result.push(`Query: ${(0, ansi_1.bold)(query, formatter)}`);
-        let timing = -1;
-        // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
-        for (const [key, value] of Object.entries(queryResults)) {
-            if (key === '.meta') {
-                timing = value.timing;
-                continue;
-            }
-            result.push(` ╰ ${key}: ${JSON.stringify(value)}`);
-        }
-        result.push(`  - Took ${(0, time_1.printAsMs)(timing, 0)}`);
-    }
-    result.push((0, ansi_1.italic)(`All queries together required ≈${(0, time_1.printAsMs)(results['.meta'].timing, 0)} (1ms accuracy, total ${(0, time_1.printAsMs)(totalInMs, 0)})`, formatter));
-    return formatter.format(result.join('\n'));
-}
 exports.queryCommand = {
     description: `Query the given R code, start with '${retriever_1.fileProtocol}' to indicate a file. The query is to be a valid query in json format (use 'help' to get more information).`,
     usageExample: ':query "<query>" <code>',
@@ -205,7 +64,7 @@ exports.queryCommand = {
         const results = await processQueryArgs(remainingLine, shell, output);
         const totalEnd = Date.now();
         if (results) {
-            output.stdout(asciiSummaryOfQueryResult(output.formatter, totalEnd - totalStart, results.query, results.processed));
+            output.stdout((0, query_print_1.asciiSummaryOfQueryResult)(ansi_1.ansiFormatter, totalEnd - totalStart, results.query, results.processed));
         }
     }
 };

package/cli/repl/server/connection.js

@@ -74,6 +74,9 @@ class FlowRServerConnection {
         this.logger = server_1.serverLog.getSubLogger({ name });
         this.socket.on('data', data => this.handleData(String(data)));
         this.socket.on('error', e => this.logger.error(`[${this.name}] Error while handling connection: ${String(e)}`));
+        this.socket.on('close', () => {
+            this.fileMap.clear();
+        });
         this.allowRSessionAccess = allowRSessionAccess;
     }
     currentMessageBuffer = '';
@@ -129,6 +132,8 @@ class FlowRServerConnection {
         this.logger.info(`[${this.name}] Received file analysis request for ${message.filename ?? 'unknown file'}${message.filetoken ? ' with token: ' + message.filetoken : ''}`);
         if (message.filetoken && this.fileMap.has(message.filetoken)) {
             this.logger.warn(`File token ${message.filetoken} already exists. Overwriting.`);
+            // explicitly delete the previous store
+            this.fileMap.delete(message.filetoken);
         }
         const tempFile = tmp.fileSync({ postfix: '.R' });
         const slicer = this.createPipelineExecutorForRequest(message, tempFile.name);
@@ -307,7 +312,7 @@ class FlowRServerConnection {
             return;
         }
         const request = requestResult.message;
-        this.logger.info(`[${this.name}] Received query request for query ${JSON.stringify(request.query)}`);
+        this.logger.info(`[${this.name}] Received query request`);
         const fileInformation = this.fileMap.get(request.filetoken);
         if (!fileInformation) {
             (0, send_1.sendMessage)(this.socket, {

package/cli/repl/server/messages/message-query.js

@@ -5,14 +5,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.responseQueryMessage = exports.requestQueryMessage = void 0;
 const joi_1 = __importDefault(require("joi"));
-const query_schema_1 = require("../../../../queries/query-schema");
+const query_1 = require("../../../../queries/query");
 exports.requestQueryMessage = {
     type: 'request-query',
     schema: joi_1.default.object({
         type: joi_1.default.string().valid('request-query').required().description('The type of the message.'),
         id: joi_1.default.string().optional().description('If you give the id, the response will be sent to the client with the same id.'),
         filetoken: joi_1.default.string().required().description('The filetoken of the file/data retrieved from the analysis request.'),
-        query: query_schema_1.QueriesSchema.required().description('The query to run on the file analysis information.')
+        query: query_1.QueriesSchema.required().description('The query to run on the file analysis information.')
     }).description('Request a query to be run on the file analysis information.')
 };
 exports.responseQueryMessage = {

package/cli/repl/server/net.js

@@ -17,7 +17,7 @@ class WebSocketServerWrapper {
         this.connectHandler = handler;
     }
     start(port) {
-        this.server = new ws_1.WebSocketServer({ port });
+        this.server = new ws_1.WebSocketServer({ port, maxPayload: 1024 * 1024 * 1024 * 1024 });
         server_1.serverLog.info('WebSocket-Server wrapper is active!');
         this.server.on('connection', c => this.connectHandler?.(new WebSocketWrapper(c)));
     }

package/cli/repl/server/send.js

@@ -2,16 +2,13 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getUnnamedSocketName = getUnnamedSocketName;
 exports.sendMessage = sendMessage;
-const server_1 = require("./server");
 const json_1 = require("../../../util/json");
 function getUnnamedSocketName(c) {
     return `${c.remoteAddress ?? '?'}@${c.remotePort ?? '?'}`;
 }
 function sendMessage(c, message) {
-    const msg = JSON.stringify(message, json_1.jsonReplacer);
-    if (server_1.serverLog.settings.minLevel >= 2 /* LogLevel.Debug */) {
-        server_1.serverLog.debug(`[${getUnnamedSocketName(c)}] sending message: ${msg}`);
-    }
-    c.write(`${msg}\n`);
+    return (0, json_1.superBigJsonStringify)(message, '\n', msg => {
+        c.write(msg);
+    });
 }
 //# sourceMappingURL=send.js.map

package/cli/repl/server/server.d.ts

@@ -11,9 +11,9 @@ export declare class FlowRServer {
     private readonly server;
     private readonly shell;
     private versionInformation;
-    private allowRSessionAccess;
+    private readonly allowRSessionAccess;
     /** maps names to the respective connection */
-    private connections;
+    private readonly connections;
     private nameCounter;
     constructor(shell: RShell, allowRSessionAccess: boolean, server?: Server);
     start(port: number): Promise<void>;

package/cli/repl/server/server.js

@@ -17,7 +17,7 @@ class FlowRServer {
     server;
     shell;
     versionInformation;
-    allowRSessionAccess = false;
+    allowRSessionAccess;
     /** maps names to the respective connection */
     connections = new Map();
     nameCounter = 0;

package/config.js

@@ -41,7 +41,7 @@ exports.flowrConfigFileSchema = joi_1.default.object({
 // we don't load from a config file at all by default unless setConfigFile is called
 let configFile = undefined;
 let configWorkingDirectory = process.cwd();
-let currentConfig;
+let currentConfig = undefined;
 function setConfigFile(file, workingDirectory = process.cwd(), forceLoad = false) {
     configFile = file;
     configWorkingDirectory = workingDirectory;

package/core/pipeline-executor.js

@@ -169,9 +169,10 @@ class PipelineExecutor {
      * _Without `expectedStepName`, please refrain from accessing the result, as you have no safeguards if the pipeline changes._
      */
     async nextStep(expectedStepName) {
+        const start = Date.now();
         const [step, result] = this._doNextStep(expectedStepName);
         const awaitedResult = await result;
-        this.output[step] = awaitedResult;
+        this.output[step] = { ...awaitedResult, '.meta': { timing: Date.now() - start } };
         this.stepCounter++;
         return { name: step, result: awaitedResult };
     }

package/core/steps/all/core/00-parse.d.ts

@@ -1,16 +1,20 @@
 import { internalPrinter } from '../../../print/print';
-import { parseToQuads } from '../../../print/parse-printer';
 import { PipelineStepStage } from '../../pipeline-step';
 import type { RShellExecutor } from '../../../../r-bridge/shell-executor';
 import type { RShell } from '../../../../r-bridge/shell';
 import type { RParseRequests } from '../../../../r-bridge/retriever';
+import type { QuadSerializationConfiguration } from '../../../../util/quads';
 export interface ParseRequiredInput {
     /** This is the {@link RShell} or {@link RShellExecutor} connection to be used to obtain the original parses AST of the R code */
     readonly shell: RShell | RShellExecutor;
     /** The request which essentially indicates the input to extract the AST from */
     readonly request: RParseRequests;
 }
-declare function processor(_results: unknown, input: Partial<ParseRequiredInput>): Promise<string>;
+export interface ParseStepOutput {
+    /** The parsed AST of the R code as given by the R parse side */
+    readonly parsed: string;
+}
+declare function processor(_results: unknown, input: Partial<ParseRequiredInput>): Promise<ParseStepOutput>;
 export declare const PARSE_WITH_R_SHELL_STEP: {
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
@@ -19,8 +23,11 @@ export declare const PARSE_WITH_R_SHELL_STEP: {
     readonly executed: PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof internalPrinter;
-        readonly 2: (text: string) => string;
-        readonly 5: typeof parseToQuads;
+        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 }: ParseStepOutput, config: QuadSerializationConfiguration) => string;
     };
     readonly dependencies: readonly [];
     readonly requiredInput: ParseRequiredInput;

package/core/steps/all/core/00-parse.js

@@ -4,13 +4,13 @@ exports.PARSE_WITH_R_SHELL_STEP = void 0;
 const print_1 = require("../../../print/print");
 const parse_printer_1 = require("../../../print/parse-printer");
 const retriever_1 = require("../../../../r-bridge/retriever");
-function processor(_results, input) {
+async function processor(_results, input) {
     /* in the future, we want to expose all cases */
     if (Array.isArray(input.request)) {
-        return (0, retriever_1.retrieveParseDataFromRCode)(input.request[0], input.shell);
+        return { parsed: await (0, retriever_1.retrieveParseDataFromRCode)(input.request[0], input.shell) };
     }
     else {
-        return (0, retriever_1.retrieveParseDataFromRCode)(input.request, input.shell);
+        return { parsed: await (0, retriever_1.retrieveParseDataFromRCode)(input.request, input.shell) };
     }
 }
 exports.PARSE_WITH_R_SHELL_STEP = {
@@ -21,8 +21,8 @@ exports.PARSE_WITH_R_SHELL_STEP = {
     executed: 0 /* PipelineStepStage.OncePerFile */,
     printer: {
         [0 /* StepOutputFormat.Internal */]: print_1.internalPrinter,
-        [2 /* StepOutputFormat.Json */]: text => text,
-        [5 /* StepOutputFormat.RdfQuads */]: parse_printer_1.parseToQuads
+        [2 /* StepOutputFormat.Json */]: JSON.stringify,
+        [5 /* StepOutputFormat.RdfQuads */]: ({ parsed }, config) => (0, parse_printer_1.parseToQuads)(parsed, config)
     },
     dependencies: [],
     requiredInput: undefined

package/core/steps/all/core/10-normalize.d.ts

@@ -3,12 +3,13 @@ import { normalizedAstToJson, normalizedAstToQuads, printNormalizedAstToMermaid,
 import { PipelineStepStage } from '../../pipeline-step';
 import type { IdGenerator } from '../../../../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { NoInfo } from '../../../../r-bridge/lang-4.x/ast/model/model';
+import type { ParseStepOutput } from './00-parse';
 export interface NormalizeRequiredInput {
     /** This id generator is only necessary if you want to retrieve a dataflow from the parsed R AST, it determines the id generator to use and by default uses the {@link deterministicCountingIdGenerator}*/
     readonly getId?: IdGenerator<NoInfo>;
 }
 declare function processor(results: {
-    parse?: string;
+    parse?: ParseStepOutput;
 }, input: Partial<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>>;
 export declare const NORMALIZE: {
     readonly name: "normalize";

package/core/steps/all/core/20-dataflow.d.ts

@@ -3,14 +3,14 @@ import { PipelineStepStage } from '../../pipeline-step';
 import { dataflowGraphToJson, dataflowGraphToMermaid, dataflowGraphToMermaidUrl, dataflowGraphToQuads } from '../../../print/dataflow-printer';
 import type { NormalizedAst } from '../../../../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { RParseRequests } from '../../../../r-bridge/retriever';
-declare function legacyProcessor(results: {
+declare function processor(results: {
     normalize?: NormalizedAst;
 }, input: {
     request?: RParseRequests;
 }): import("../../../../dataflow/info").DataflowInformation;
 export declare const STATIC_DATAFLOW: {
     readonly humanReadableName: "dataflow";
-    readonly processor: typeof legacyProcessor;
+    readonly processor: typeof processor;
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";

package/core/steps/all/core/20-dataflow.js

@@ -17,13 +17,13 @@ const staticDataflowCommon = {
     },
     dependencies: ['normalize'],
 };
-function legacyProcessor(results, input) {
+function processor(results, input) {
     return (0, extractor_1.produceDataFlowGraph)(input.request, results.normalize);
 }
 exports.STATIC_DATAFLOW = {
     ...staticDataflowCommon,
     humanReadableName: 'dataflow',
-    processor: legacyProcessor,
+    processor,
     requiredInput: {}
 };
 //# sourceMappingURL=20-dataflow.js.map

package/core/steps/pipeline/default-pipelines.d.ts

@@ -2,12 +2,15 @@ export declare const DEFAULT_SLICING_PIPELINE: import("./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("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<import("../all/core/00-parse").ParseStepOutput>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
-        readonly 2: (text: string) => string;
-        readonly 5: typeof import("../../print/parse-printer").parseToQuads;
+        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("../all/core/00-parse").ParseStepOutput, config: import("../../../util/quads").QuadSerializationConfiguration) => string;
     };
     readonly dependencies: readonly [];
     readonly requiredInput: import("../all/core/00-parse").ParseRequiredInput;
@@ -16,7 +19,7 @@ export declare const DEFAULT_SLICING_PIPELINE: import("./pipeline").Pipeline<{
     readonly humanReadableName: "normalize";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        parse?: string;
+        parse?: import("../all/core/00-parse").ParseStepOutput;
     }, input: Partial<import("../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("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -80,12 +83,15 @@ export declare const DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE: import("./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("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<import("../all/core/00-parse").ParseStepOutput>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
-        readonly 2: (text: string) => string;
-        readonly 5: typeof import("../../print/parse-printer").parseToQuads;
+        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("../all/core/00-parse").ParseStepOutput, config: import("../../../util/quads").QuadSerializationConfiguration) => string;
     };
     readonly dependencies: readonly [];
     readonly requiredInput: import("../all/core/00-parse").ParseRequiredInput;
@@ -94,7 +100,7 @@ export declare const DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE: import("./pipeline"
     readonly humanReadableName: "normalize";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        parse?: string;
+        parse?: import("../all/core/00-parse").ParseStepOutput;
     }, input: Partial<import("../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("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -158,12 +164,15 @@ export declare const DEFAULT_SLICE_WITHOUT_RECONSTRUCT_PIPELINE: import("./pipel
     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("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<import("../all/core/00-parse").ParseStepOutput>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
-        readonly 2: (text: string) => string;
-        readonly 5: typeof import("../../print/parse-printer").parseToQuads;
+        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("../all/core/00-parse").ParseStepOutput, config: import("../../../util/quads").QuadSerializationConfiguration) => string;
     };
     readonly dependencies: readonly [];
     readonly requiredInput: import("../all/core/00-parse").ParseRequiredInput;
@@ -172,7 +181,7 @@ export declare const DEFAULT_SLICE_WITHOUT_RECONSTRUCT_PIPELINE: import("./pipel
     readonly humanReadableName: "normalize";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        parse?: string;
+        parse?: import("../all/core/00-parse").ParseStepOutput;
     }, input: Partial<import("../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("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -222,12 +231,15 @@ export declare const DEFAULT_DATAFLOW_PIPELINE: import("./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("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<import("../all/core/00-parse").ParseStepOutput>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
-        readonly 2: (text: string) => string;
-        readonly 5: typeof import("../../print/parse-printer").parseToQuads;
+        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("../all/core/00-parse").ParseStepOutput, config: import("../../../util/quads").QuadSerializationConfiguration) => string;
     };
     readonly dependencies: readonly [];
     readonly requiredInput: import("../all/core/00-parse").ParseRequiredInput;
@@ -236,7 +248,7 @@ export declare const DEFAULT_DATAFLOW_PIPELINE: import("./pipeline").Pipeline<{
     readonly humanReadableName: "normalize";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        parse?: string;
+        parse?: import("../all/core/00-parse").ParseStepOutput;
     }, input: Partial<import("../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("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -272,12 +284,15 @@ export declare const DEFAULT_NORMALIZE_PIPELINE: import("./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("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<import("../all/core/00-parse").ParseStepOutput>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
-        readonly 2: (text: string) => string;
-        readonly 5: typeof import("../../print/parse-printer").parseToQuads;
+        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("../all/core/00-parse").ParseStepOutput, config: import("../../../util/quads").QuadSerializationConfiguration) => string;
     };
     readonly dependencies: readonly [];
     readonly requiredInput: import("../all/core/00-parse").ParseRequiredInput;
@@ -286,7 +301,7 @@ export declare const DEFAULT_NORMALIZE_PIPELINE: import("./pipeline").Pipeline<{
     readonly humanReadableName: "normalize";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        parse?: string;
+        parse?: import("../all/core/00-parse").ParseStepOutput;
     }, input: Partial<import("../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("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -303,12 +318,15 @@ export declare const DEFAULT_PARSE_PIPELINE: import("./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("../all/core/00-parse").ParseRequiredInput>) => Promise<string>;
+    readonly processor: (_results: unknown, input: Partial<import("../all/core/00-parse").ParseRequiredInput>) => Promise<import("../all/core/00-parse").ParseStepOutput>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
         readonly 0: typeof import("../../print/print").internalPrinter;
-        readonly 2: (text: string) => string;
-        readonly 5: typeof import("../../print/parse-printer").parseToQuads;
+        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("../all/core/00-parse").ParseStepOutput, config: import("../../../util/quads").QuadSerializationConfiguration) => string;
     };
     readonly dependencies: readonly [];
     readonly requiredInput: import("../all/core/00-parse").ParseRequiredInput;