@eagleoutice/flowr 2.1.0 → 2.1.2

package/README.md

@@ -24,7 +24,8 @@ You can enter `:help` to gain more information on its capabilities.
 
 ## 📜 More Information
 
-For more details on how to use _flowR_ please refer to the the [wiki pages](https://github.com/flowr-analysis/flowr/wiki), as well as the deployed [code documentation](https://flowr-analysis.github.io/flowr/doc/).
+For more details on how to use _flowR_ please refer to the [wiki pages](https://github.com/flowr-analysis/flowr/wiki),
+as well as the deployed [code documentation](https://flowr-analysis.github.io/flowr/doc/).
 
 ## 🚀 Contributing
 

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

@@ -3,22 +3,18 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseCommand = void 0;
 const pipeline_executor_1 = require("../../../core/pipeline-executor");
 const format_1 = require("../../../r-bridge/lang-4.x/ast/parser/json/format");
-const parser_1 = require("../../../r-bridge/lang-4.x/ast/parser/json/parser");
-const input_format_1 = require("../../../r-bridge/lang-4.x/ast/parser/xml/input-format");
-const type_1 = require("../../../r-bridge/lang-4.x/ast/model/type");
-const normalize_meta_1 = require("../../../r-bridge/lang-4.x/ast/parser/xml/normalize-meta");
+const normalize_meta_1 = require("../../../r-bridge/lang-4.x/ast/parser/main/normalize-meta");
 const default_pipelines_1 = require("../../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../../r-bridge/retriever");
-function toDepthMap(xml) {
-    const root = (0, input_format_1.getKeyGuarded)(xml, type_1.RawRType.ExpressionList);
-    const visit = [{ depth: 0, node: root }];
+function toDepthMap(entry) {
+    const visit = [{ depth: 0, node: entry }];
     const result = [];
     while (visit.length > 0) {
         const current = visit.pop();
         if (current === undefined) {
             continue;
         }
-        const children = current.node[input_format_1.childrenKey] ?? [];
+        const children = current.node.children;
         result.push({ ...current, leaf: children.length === 0 });
         children.reverse();
         const nextDepth = current.depth + 1;
@@ -75,13 +71,8 @@ function depthListToTextTree(list, f) {
         deadDepths.delete(depth);
         result += initialIndentation(i, depth, deadDepths, nextDepth, list, f);
         result += f.reset();
-        const raw = (0, normalize_meta_1.objectWithArrUnwrap)(node);
-        const content = raw[input_format_1.contentKey];
-        const locationRaw = raw[input_format_1.attributesKey];
-        let location = '';
-        if (locationRaw !== undefined) {
-            location = retrieveLocationString(locationRaw);
-        }
+        const content = node.text;
+        const location = retrieveLocationString(node);
         const type = (0, normalize_meta_1.getTokenType)(node);
         if (leaf) {
             const suffix = `${f.format(content ? JSON.stringify(content) : '', { style: 1 /* FontStyles.Bold */ })}${f.format(location, { style: 3 /* FontStyles.Italic */ })}`;
@@ -104,7 +95,7 @@ exports.parseCommand = {
             shell,
             request: (0, retriever_1.requestFromInput)((0, retriever_1.removeRQuotes)(remainingLine.trim()))
         }).allRemainingSteps();
-        const object = (0, parser_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(result.parse));
+        const object = (0, format_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(result.parse));
         output.stdout(depthListToTextTree(toDepthMap(object), output.formatter));
     }
 };

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

@@ -12,6 +12,10 @@ 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");
 async function getDataflow(shell, remainingLine) {
     return await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
         shell,
@@ -99,6 +103,21 @@ function asciiCallContext(formatter, results, 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)) {
@@ -107,10 +126,60 @@ function asciiSummaryOfQueryResult(formatter, totalInMs, results, processed) {
         }
         if (query === 'call-context') {
             const out = queryResults;
-            result.push(`Query: ${(0, ansi_1.bold)(query, formatter)} (${out['.meta'].timing.toFixed(0)}ms)`);
+            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
@@ -121,9 +190,9 @@ function asciiSummaryOfQueryResult(formatter, totalInMs, results, processed) {
             }
             result.push(` ╰ ${key}: ${JSON.stringify(value)}`);
         }
-        result.push(`  - Took ${timing.toFixed(0)}ms`);
+        result.push(`  - Took ${(0, time_1.printAsMs)(timing, 0)}`);
     }
-    result.push((0, ansi_1.italic)(`All queries together required ≈${results['.meta'].timing.toFixed(0)}ms (1ms accuracy, total ${totalInMs.toFixed(0)}ms)`, formatter));
+    result.push((0, ansi_1.italic)(`All queries together required ≈${(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 = {

package/core/print/parse-printer.js

@@ -2,29 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseToQuads = parseToQuads;
 const quads_1 = require("../../util/quads");
-const parser_1 = require("../../r-bridge/lang-4.x/ast/parser/json/parser");
 const format_1 = require("../../r-bridge/lang-4.x/ast/parser/json/format");
-const input_format_1 = require("../../r-bridge/lang-4.x/ast/parser/xml/input-format");
-function filterObject(obj, keys) {
-    if (typeof obj !== 'object') {
-        return obj;
-    }
-    else if (Array.isArray(obj)) {
-        return obj.map(e => filterObject(e, keys));
-    }
-    if (Object.keys(obj).some(k => keys.has(k))) {
-        return Object.fromEntries(Object.entries(obj)
-            .filter(([k]) => keys.has(k))
-            .map(([k, v]) => [k, filterObject(v, keys)]));
-    }
-    else {
-        return Object.fromEntries(Object.entries(obj)
-            .map(([k, v]) => [k, filterObject(v, keys)]));
-    }
-}
 function parseToQuads(code, config) {
-    const obj = (0, parser_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(code));
-    // recursively filter so that if the object contains one of the keys 'a', 'b' or 'c', all other keys are ignored
-    return (0, quads_1.serialize2quads)(filterObject(obj, new Set([input_format_1.attributesKey, input_format_1.childrenKey, input_format_1.contentKey])), config);
+    return (0, quads_1.serialize2quads)((0, format_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(code)), config);
 }
 //# sourceMappingURL=parse-printer.js.map

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

@@ -154,6 +154,70 @@ export declare const DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE: import("./pipeline"
     readonly dependencies: readonly ["slice"];
     readonly requiredInput: import("../all/static-slicing/10-reconstruct").ReconstructRequiredInput;
 }>;
+export declare const DEFAULT_SLICE_WITHOUT_RECONSTRUCT_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 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 dependencies: readonly [];
+    readonly requiredInput: import("../all/core/00-parse").ParseRequiredInput;
+} | {
+    readonly name: "normalize";
+    readonly humanReadableName: "normalize";
+    readonly description: "Normalize the AST to flowR's AST";
+    readonly processor: (results: {
+        parse?: string;
+    }, 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: {
+        readonly 0: typeof import("../../print/print").internalPrinter;
+        readonly 2: typeof import("../../print/normalize-printer").normalizedAstToJson;
+        readonly 5: typeof import("../../print/normalize-printer").normalizedAstToQuads;
+        readonly 3: typeof import("../../print/normalize-printer").printNormalizedAstToMermaid;
+        readonly 4: typeof import("../../print/normalize-printer").printNormalizedAstToMermaidUrl;
+    };
+    readonly dependencies: readonly ["parse"];
+    readonly requiredInput: import("../all/core/10-normalize").NormalizeRequiredInput;
+} | {
+    readonly humanReadableName: "dataflow";
+    readonly processor: (results: {
+        normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+    }, input: {
+        request?: import("../../../r-bridge/retriever").RParseRequests;
+    }) => import("../../../dataflow/info").DataflowInformation;
+    readonly requiredInput: {};
+    readonly name: "dataflow";
+    readonly description: "Construct the dataflow graph";
+    readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
+    readonly printer: {
+        readonly 0: typeof import("../../print/print").internalPrinter;
+        readonly 2: typeof import("../../print/dataflow-printer").dataflowGraphToJson;
+        readonly 5: typeof import("../../print/dataflow-printer").dataflowGraphToQuads;
+        readonly 3: typeof import("../../print/dataflow-printer").dataflowGraphToMermaid;
+        readonly 4: typeof import("../../print/dataflow-printer").dataflowGraphToMermaidUrl;
+    };
+    readonly dependencies: readonly ["normalize"];
+} | {
+    readonly name: "slice";
+    readonly humanReadableName: "static slice";
+    readonly description: "Calculate the actual static slice from the dataflow graph and the given slicing criteria";
+    readonly processor: (results: {
+        dataflow?: import("../../../dataflow/info").DataflowInformation;
+        normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+    }, input: Partial<import("../all/static-slicing/00-slice").SliceRequiredInput>) => Readonly<import("../../../slicing/static/slicer-types").SliceResult>;
+    readonly executed: import("../pipeline-step").PipelineStepStage.OncePerRequest;
+    readonly printer: {
+        readonly 0: typeof import("../../print/print").internalPrinter;
+    };
+    readonly dependencies: readonly ["dataflow"];
+    readonly requiredInput: import("../all/static-slicing/00-slice").SliceRequiredInput;
+}>;
 export declare const DEFAULT_DATAFLOW_PIPELINE: import("./pipeline").Pipeline<{
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";

package/core/steps/pipeline/default-pipelines.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DEFAULT_PARSE_PIPELINE = exports.DEFAULT_NORMALIZE_PIPELINE = exports.DEFAULT_DATAFLOW_PIPELINE = exports.DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE = exports.DEFAULT_SLICING_PIPELINE = void 0;
+exports.DEFAULT_PARSE_PIPELINE = exports.DEFAULT_NORMALIZE_PIPELINE = exports.DEFAULT_DATAFLOW_PIPELINE = exports.DEFAULT_SLICE_WITHOUT_RECONSTRUCT_PIPELINE = exports.DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE = exports.DEFAULT_SLICING_PIPELINE = void 0;
 /**
  * Contains the default pipeline for working with flowr
  */
@@ -12,6 +12,7 @@ const _00_slice_1 = require("../all/static-slicing/00-slice");
 const _10_reconstruct_1 = require("../all/static-slicing/10-reconstruct");
 exports.DEFAULT_SLICING_PIPELINE = (0, pipeline_1.createPipeline)(_00_parse_1.PARSE_WITH_R_SHELL_STEP, _10_normalize_1.NORMALIZE, _20_dataflow_1.STATIC_DATAFLOW, _00_slice_1.STATIC_SLICE, _10_reconstruct_1.NAIVE_RECONSTRUCT);
 exports.DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE = exports.DEFAULT_SLICING_PIPELINE;
+exports.DEFAULT_SLICE_WITHOUT_RECONSTRUCT_PIPELINE = (0, pipeline_1.createPipeline)(_00_parse_1.PARSE_WITH_R_SHELL_STEP, _10_normalize_1.NORMALIZE, _20_dataflow_1.STATIC_DATAFLOW, _00_slice_1.STATIC_SLICE);
 exports.DEFAULT_DATAFLOW_PIPELINE = (0, pipeline_1.createPipeline)(_00_parse_1.PARSE_WITH_R_SHELL_STEP, _10_normalize_1.NORMALIZE, _20_dataflow_1.STATIC_DATAFLOW);
 exports.DEFAULT_NORMALIZE_PIPELINE = (0, pipeline_1.createPipeline)(_00_parse_1.PARSE_WITH_R_SHELL_STEP, _10_normalize_1.NORMALIZE);
 exports.DEFAULT_PARSE_PIPELINE = (0, pipeline_1.createPipeline)(_00_parse_1.PARSE_WITH_R_SHELL_STEP);

package/dataflow/cluster.d.ts

@@ -0,0 +1,20 @@
+import type { DataflowGraph } from './graph/graph';
+import type { NodeId } from '../r-bridge/lang-4.x/ast/model/processing/node-id';
+export type DataflowGraphClusters = DataflowGraphCluster[];
+export interface DataflowGraphCluster {
+    /**
+     * The node which started the cluster,
+     * as this is theoretically picked random, there are just two guarantees you can rely on:
+     *
+     * 1. The node is part of the `members` as well
+     * 2. At one point during the clustering, the node wsa considered as a starting point
+     *
+     * In general, this is more of a debugging aid/representative of the cluster.
+     */
+    readonly startNode: NodeId;
+    /** All nodes that are part of this cluster */
+    readonly members: readonly NodeId[];
+    /** If the cluster contains unknown side effects */
+    readonly hasUnknownSideEffects: boolean;
+}
+export declare function findAllClusters(graph: DataflowGraph): DataflowGraphClusters;

package/dataflow/cluster.js

@@ -0,0 +1,46 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.findAllClusters = findAllClusters;
+const edge_1 = require("./graph/edge");
+const vertex_1 = require("./graph/vertex");
+const assert_1 = require("../util/assert");
+function findAllClusters(graph) {
+    const clusters = [];
+    // we reverse the vertices since dependencies usually point "backwards" from later nodes
+    const notReached = new Set([...graph.vertices(true)].map(([id]) => id).reverse());
+    while (notReached.size > 0) {
+        const [startNode] = notReached;
+        notReached.delete(startNode);
+        clusters.push({
+            startNode: startNode,
+            members: [...makeCluster(graph, startNode, notReached)],
+            hasUnknownSideEffects: graph.unknownSideEffects.has(startNode)
+        });
+    }
+    return clusters;
+}
+function makeCluster(graph, from, notReached) {
+    const info = graph.getVertex(from);
+    (0, assert_1.guard)(info !== undefined, () => `Vertex ${from} not found in graph`);
+    const nodes = new Set([from]);
+    // cluster function def exit points
+    if (info.tag === vertex_1.VertexType.FunctionDefinition) {
+        for (const sub of info.exitPoints) {
+            if (notReached.delete(sub)) {
+                makeCluster(graph, sub, notReached).forEach(n => nodes.add(n));
+            }
+        }
+    }
+    // cluster adjacent edges
+    for (const [dest, { types }] of [...graph.outgoingEdges(from) ?? [], ...graph.ingoingEdges(from) ?? []]) {
+        // don't cluster for function content if it isn't returned
+        if ((0, edge_1.edgeDoesNotIncludeType)(types, edge_1.EdgeType.Returns) && info.onlyBuiltin && info.name == '{') {
+            continue;
+        }
+        if (notReached.delete(dest)) {
+            makeCluster(graph, dest, notReached).forEach(n => nodes.add(n));
+        }
+    }
+    return nodes;
+}
+//# sourceMappingURL=cluster.js.map

package/dataflow/graph/edge.d.ts

@@ -1,7 +1,6 @@
 /**
- * An edge consist of:
- * - the target node (i.e., the variable or processing node),
- * - a type (if it is read or used in the context), and
+ * An edge consist of only of the type (source and target are encoded with the Dataflow Graph).
+ * Multiple edges are encoded by joining the respective type bits.
  */
 export interface DataflowGraphEdge {
     types: EdgeTypeBits;

package/dataflow/graph/graph.d.ts

@@ -59,7 +59,7 @@ export interface DataflowGraphJson {
 export declare class DataflowGraph<Vertex extends DataflowGraphVertexInfo = DataflowGraphVertexInfo, Edge extends DataflowGraphEdge = DataflowGraphEdge> {
     private static DEFAULT_ENVIRONMENT;
     private _idMap;
-    private _unknownSideEffects;
+    private readonly _unknownSideEffects;
     constructor(idMap: AstIdMap | undefined);
     /** Contains the vertices of the root level graph (i.e., included those vertices from the complete graph, that are nested within function definitions) */
     protected rootVertices: Set<NodeId>;

package/documentation/data/server/doc-data-server-messages.d.ts

@@ -1 +1 @@
-export declare function documentAllMessages(): void;
+export declare function documentAllServerMessages(): void;

package/documentation/data/server/doc-data-server-messages.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.documentAllMessages = documentAllMessages;
+exports.documentAllServerMessages = documentAllServerMessages;
 const doc_server_message_1 = require("../../doc-util/doc-server-message");
 const message_hello_1 = require("../../../cli/repl/server/messages/message-hello");
 const shell_1 = require("../../../r-bridge/shell");
@@ -16,9 +16,10 @@ const message_slice_1 = require("../../../cli/repl/server/messages/message-slice
 const message_repl_1 = require("../../../cli/repl/server/messages/message-repl");
 const message_query_1 = require("../../../cli/repl/server/messages/message-query");
 const example_query_code_1 = require("../query/example-query-code");
-const call_context_query_format_1 = require("../../../queries/call-context-query/call-context-query-format");
+const call_context_query_format_1 = require("../../../queries/catalog/call-context-query/call-context-query-format");
 const message_lineage_1 = require("../../../cli/repl/server/messages/message-lineage");
-function documentAllMessages() {
+const doc_structure_1 = require("../../doc-util/doc-structure");
+function documentAllServerMessages() {
     (0, doc_server_message_1.documentServerMessage)({
         title: 'Hello',
         type: 'response',
@@ -217,9 +218,14 @@ While the context is derived from the \`filename\`, we currently offer no way to
     end
     deactivate  Server
 	`,
-        shortDescription: 'The server slices a file based on the given criteria.',
+        shortDescription: `([DEPRECATED](${doc_files_1.FlowrWikiBaseRef}/Query%20API)) The server slices a file based on the given criteria.`,
         text: async (shell) => {
             return `
+${(0, doc_structure_1.block)({
+                type: 'WARNING',
+                content: `We deprecated the slice request in favor of the \`static-slice\` [Query](${doc_files_1.FlowrWikiBaseRef}/Query%20API).`
+            })}
+
 To slice, you have to send a file analysis request first. The \`filetoken\` you assign is of use here as you can re-use it to repeatedly slice the same file.
 Besides that, you only need to add an array of slicing criteria, using one of the formats described on the [terminology wiki page](${doc_files_1.FlowrWikiBaseRef}/Terminology#slicing-criterion) 
 (however, instead of using \`;\`, you can simply pass separate array elements).

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

@@ -1 +1,2 @@
 export declare function codeBlock(language: string, code: string | undefined): string;
+export declare function jsonWithLimit(object: object, maxLength?: number, tooLongText?: string): string;

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

@@ -1,7 +1,16 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.codeBlock = codeBlock;
+exports.jsonWithLimit = jsonWithLimit;
+const json_1 = require("../../util/json");
 function codeBlock(language, code) {
     return `\n\`\`\`${language}\n${code?.trim() ?? ''}\n\`\`\`\n`;
 }
+function jsonWithLimit(object, maxLength = 5_000, tooLongText = '_As the code is pretty long, we inhibit pretty printing and syntax highlighting (JSON):_') {
+    const prettyPrinted = JSON.stringify(object, json_1.jsonReplacer, 2);
+    return `
+${prettyPrinted.length > maxLength ? tooLongText : ''}
+${codeBlock(prettyPrinted.length > maxLength ? 'text' : 'json', prettyPrinted.length > 5_000 ? JSON.stringify(object, json_1.jsonReplacer) : prettyPrinted)}
+`;
+}
 //# sourceMappingURL=doc-code.js.map

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

@@ -10,6 +10,7 @@ export interface PrintDataflowGraphOptions {
     readonly codeOpen?: boolean;
     readonly exposeResult?: boolean;
     readonly switchCodeAndGraph?: boolean;
+    readonly hideEnvInMermaid?: boolean;
 }
 export declare function printDfGraphForCode(shell: RShell, code: string, options: PrintDataflowGraphOptions & {
     exposeResult: true;

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

@@ -11,8 +11,8 @@ const decorate_1 = require("../../r-bridge/lang-4.x/ast/model/processing/decorat
 const resolve_graph_1 = require("../../dataflow/graph/resolve-graph");
 const diff_1 = require("../../dataflow/graph/diff");
 const assert_1 = require("../../util/assert");
-const doc_ms_1 = require("./doc-ms");
 const json_1 = require("../../util/json");
+const time_1 = require("../../util/time");
 function printDfGraph(graph, mark) {
     return `
 \`\`\`mermaid
@@ -24,7 +24,7 @@ ${(0, dfg_1.graphToMermaid)({
 \`\`\`
 	`;
 }
-async function printDfGraphForCode(shell, code, { mark, showCode = true, codeOpen = false, exposeResult, switchCodeAndGraph = false } = {}) {
+async function printDfGraphForCode(shell, code, { mark, showCode = true, codeOpen = false, exposeResult, switchCodeAndGraph = false, hideEnvInMermaid = false } = {}) {
     const now = performance.now();
     const result = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
         shell,
@@ -34,7 +34,7 @@ async function printDfGraphForCode(shell, code, { mark, showCode = true, codeOpe
     if (switchCodeAndGraph) {
         (0, assert_1.guard)(showCode, 'can not switch code and graph if code is not shown');
     }
-    const metaInfo = `The analysis required _${(0, doc_ms_1.printAsMs)(duration)}_ (including parsing and normalization) within the generation environment.`;
+    const metaInfo = `The analysis required _${(0, time_1.printAsMs)(duration)}_ (incl. parse and normalize) within the generation environment.`;
     const dfGraph = printDfGraph(result.dataflow.graph, mark);
     let resultText = '\n\n';
     if (showCode) {
@@ -59,7 +59,8 @@ ${switchCodeAndGraph ? dfGraph : codeText}
 \`\`\`
 ${(0, dfg_1.graphToMermaid)({
             graph: result.dataflow.graph,
-            prefix: 'flowchart LR'
+            prefix: 'flowchart LR',
+            includeEnvironments: !hideEnvInMermaid
         }).string}
 \`\`\`
 

package/documentation/doc-util/doc-normalized-ast.js

@@ -10,8 +10,8 @@ const decorate_1 = require("../../r-bridge/lang-4.x/ast/model/processing/decorat
 const resolve_graph_1 = require("../../dataflow/graph/resolve-graph");
 const diff_1 = require("../../dataflow/graph/diff");
 const assert_1 = require("../../util/assert");
-const doc_ms_1 = require("./doc-ms");
 const ast_1 = require("../../util/mermaid/ast");
+const time_1 = require("../../util/time");
 function printNormalizedAst(ast, prefix = 'flowchart TD\n') {
     return `
 \`\`\`mermaid
@@ -26,7 +26,7 @@ async function printNormalizedAstForCode(shell, code, { showCode = true, prefix
         request: (0, retriever_1.requestFromInput)(code)
     }).allRemainingSteps();
     const duration = performance.now() - now;
-    const metaInfo = `The analysis required _${(0, doc_ms_1.printAsMs)(duration)}_ (including parsing) within the generation environment.`;
+    const metaInfo = `The analysis required _${(0, time_1.printAsMs)(duration)}_ (including parsing) within the generation environment.`;
     return '\n\n' + printNormalizedAst(result.normalize.ast, prefix) + (showCode ? `
 <details>
 

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

@@ -9,12 +9,13 @@ const query_1 = require("../../queries/query");
 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");
-const doc_ms_1 = require("./doc-ms");
 const json_1 = require("../../util/json");
 const ansi_1 = require("../../util/ansi");
 const repl_query_1 = require("../../cli/repl/commands/repl-query");
 const doc_files_1 = require("./doc-files");
 const doc_dfg_1 = require("./doc-dfg");
+const doc_code_1 = require("./doc-code");
+const time_1 = require("../../util/time");
 async function showQuery(shell, code, queries, { showCode, collapseResult } = {}) {
     const now = performance.now();
     const analysis = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
@@ -24,9 +25,8 @@ async function showQuery(shell, code, queries, { showCode, collapseResult } = {}
     const results = (0, query_1.executeQueries)({ graph: analysis.dataflow.graph, ast: analysis.normalize }, queries);
     const duration = performance.now() - now;
     const metaInfo = `
-The analysis required _${(0, doc_ms_1.printAsMs)(duration)}_ (including parsing and normalization and the query) within the generation environment.
+The analysis required _${(0, time_1.printAsMs)(duration)}_ (including parsing and normalization and the query) within the generation environment.
 	`.trim();
-    const resultAsString = JSON.stringify(results, json_1.jsonReplacer, 2);
     return `
 
 \`\`\`json
@@ -46,9 +46,7 @@ ${metaInfo}
 In general, the JSON contains the Ids of the nodes in question as they are present in the normalized AST or the dataflow graph of flowR.
 Please consult the [Interface](${doc_files_1.FlowrWikiBaseRef}/Interface) wiki page for more information on how to get those.
 
-\`\`\`json
-${resultAsString}
-\`\`\`
+${(0, doc_code_1.jsonWithLimit)(results)}
 
 </details>
 
@@ -79,7 +77,7 @@ function linkify(name) {
     return name.toLowerCase().replace(/ /g, '-');
 }
 function tocForQueryType(type) {
-    const queries = exports.RegisteredQueries[type];
+    const queries = [...exports.RegisteredQueries[type].entries()].sort(([, { name: a }], [, { name: b }]) => a.localeCompare(b));
     const result = [];
     for (const [id, { name, shortDescription }] of queries) {
         result.push(`1. [${name}](#${linkify(name)}) (\`${id}\`):\\\n    ${shortDescription}`);

package/documentation/doc-util/doc-server-message.js

@@ -9,8 +9,8 @@ const schema_1 = require("../../util/schema");
 const ansi_1 = require("../../util/ansi");
 const net_1 = require("../../../test/functionality/_helper/net");
 const doc_code_1 = require("./doc-code");
-const doc_ms_1 = require("./doc-ms");
 const assert_1 = require("../../util/assert");
+const time_1 = require("../../util/time");
 const messages = [];
 function documentServerMessage(description) {
     messages.push(description);
@@ -29,7 +29,6 @@ async function inServerContext(shell, fn) {
 }
 function explainMsg(msg, type, desc = '', open = false) {
     const bold = open ? s => `<b>${s}</b>` : s => s;
-    const msgPrettyPrint = JSON.stringify(msg, null, 2);
     return `
 <li> ${bold('<code>' + msg.type + `</code> (${type})`)}
 <details${open ? ' open' : ''}> 
@@ -38,8 +37,7 @@ function explainMsg(msg, type, desc = '', open = false) {
 
 ${desc}
 
-${msgPrettyPrint.length > 5_000 ? '_As the message is pretty long, we inhibit pretty printing and syntax highlighting:_' : ''}
-${(0, doc_code_1.codeBlock)(msgPrettyPrint.length > 5_000 ? 'text' : 'json', msgPrettyPrint.length > 5_000 ? JSON.stringify(msg) : msgPrettyPrint)}
+${(0, doc_code_1.jsonWithLimit)(msg)}
 
 </details>
 </li>
@@ -102,7 +100,7 @@ The following lists all messages that were sent and received in case you want to
 
 ${explainPingPong(messages, response)}
 
-The complete round-trip took ${(0, doc_ms_1.printAsMs)(end - start)} (including time required to validate the messages, start, and stop the internal mock server).
+The complete round-trip took ${(0, time_1.printAsMs)(end - start)} (including time required to validate the messages, start, and stop the internal mock server).
 
 </details>
 `;