@eagleoutice/flowr 2.1.3 → 2.1.4

package/dataflow/environments/environment.d.ts

@@ -40,5 +40,6 @@ export interface REnvironmentInformation {
     readonly level: number;
 }
 export declare const BuiltInEnvironment: Environment;
+export declare const EmptyBuiltInEnvironment: IEnvironment;
 export declare function initializeCleanEnvironments(fullBuiltIns?: boolean): REnvironmentInformation;
 export declare function builtInEnvJsonReplacer(k: unknown, v: unknown): unknown;

package/dataflow/environments/environment.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.BuiltInEnvironment = exports.Environment = void 0;
+exports.EmptyBuiltInEnvironment = exports.BuiltInEnvironment = exports.Environment = void 0;
 exports.makeReferenceMaybe = makeReferenceMaybe;
 exports.makeAllMaybe = makeAllMaybe;
 exports.initializeCleanEnvironments = initializeCleanEnvironments;
@@ -55,16 +55,16 @@ exports.Environment = Environment;
 /* the built-in environment is the root of all environments */
 exports.BuiltInEnvironment = new Environment(undefined);
 exports.BuiltInEnvironment.memory = undefined;
-const EmptyBuiltInEnvironment = {
+exports.EmptyBuiltInEnvironment = {
     id: exports.BuiltInEnvironment.id,
     memory: undefined,
     parent: undefined
 };
 function initializeCleanEnvironments(fullBuiltIns = true) {
     exports.BuiltInEnvironment.memory ??= built_in_1.BuiltInMemory;
-    EmptyBuiltInEnvironment.memory ??= built_in_1.EmptyBuiltInMemory;
+    exports.EmptyBuiltInEnvironment.memory ??= built_in_1.EmptyBuiltInMemory;
     return {
-        current: new Environment(fullBuiltIns ? exports.BuiltInEnvironment : EmptyBuiltInEnvironment),
+        current: new Environment(fullBuiltIns ? exports.BuiltInEnvironment : exports.EmptyBuiltInEnvironment),
         level: 0
     };
 }
@@ -72,7 +72,7 @@ function builtInEnvJsonReplacer(k, v) {
     if (v === exports.BuiltInEnvironment) {
         return '<BuiltInEnvironment>';
     }
-    else if (v === EmptyBuiltInEnvironment) {
+    else if (v === exports.EmptyBuiltInEnvironment) {
         return '<EmptyBuiltInEnvironment>';
     }
     else {

package/dataflow/extractor.js

@@ -17,6 +17,9 @@ const type_1 = require("../r-bridge/lang-4.x/ast/model/type");
 const retriever_1 = require("../r-bridge/retriever");
 const environment_1 = require("./environments/environment");
 const built_in_source_1 = require("./internal/process/functions/call/built-in/built-in-source");
+const cfg_1 = require("../util/cfg/cfg");
+const edge_1 = require("./graph/edge");
+const identify_link_to_last_call_relation_1 = require("../queries/catalog/call-context-query/identify-link-to-last-call-relation");
 exports.processors = {
     [type_1.RType.Number]: process_value_1.processValue,
     [type_1.RType.String]: process_value_1.processValue,
@@ -47,6 +50,25 @@ exports.processors = {
         namespace: n.grouping?.[0].content ? undefined : 'base'
     }, (0, make_argument_1.wrapArgumentsUnnamed)(n.children, d.completeAst.idMap), n.info.id, d)
 };
+function resolveLinkToSideEffects(ast, graph) {
+    let cfg = undefined;
+    for (const s of graph.unknownSideEffects) {
+        if (typeof s !== 'object') {
+            continue;
+        }
+        if (!cfg) {
+            cfg = (0, cfg_1.extractCFG)(ast).graph;
+        }
+        /* this has to change whenever we add a new link to relations because we currently offer no abstraction for the type */
+        const potentials = (0, identify_link_to_last_call_relation_1.identifyLinkToLastCallRelation)(s.id, cfg, graph, s.linkTo.callName);
+        for (const pot of potentials) {
+            graph.addEdge(s.id, pot, edge_1.EdgeType.Reads);
+        }
+        if (potentials.length > 0) {
+            graph.unknownSideEffects.delete(s);
+        }
+    }
+}
 function produceDataFlowGraph(request, ast) {
     const multifile = Array.isArray(request);
     let firstRequest;
@@ -70,6 +92,7 @@ function produceDataFlowGraph(request, ast) {
             df = (0, built_in_source_1.standaloneSourceFile)(request[i], dfData, `root-${i}`, df);
         }
     }
+    resolveLinkToSideEffects(ast, df.graph);
     return df;
 }
 //# sourceMappingURL=extractor.js.map

package/dataflow/graph/dataflowgraph-builder.d.ts

@@ -5,6 +5,7 @@ import { DataflowGraph } from './graph';
 import type { REnvironmentInformation } from '../environments/environment';
 import type { DataflowGraphVertexUse } from './vertex';
 import type { ControlDependency } from '../info';
+import type { LinkTo } from '../../queries/catalog/call-context-query/call-context-query-format';
 export declare function emptyGraph(idMap?: AstIdMap): DataflowGraphBuilder;
 export type DataflowGraphEdgeTarget = NodeId | (readonly NodeId[]);
 /**
@@ -137,3 +138,4 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      */
     overwriteRootIds(ids: readonly NodeId[]): this;
 }
+export declare function getBuiltInSideEffect(name: string): LinkTo<RegExp> | undefined;

package/dataflow/graph/dataflowgraph-builder.js

@@ -2,6 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DataflowGraphBuilder = void 0;
 exports.emptyGraph = emptyGraph;
+exports.getBuiltInSideEffect = getBuiltInSideEffect;
 const objects_1 = require("../../util/objects");
 const node_id_1 = require("../../r-bridge/lang-4.x/ast/model/processing/node-id");
 const graph_1 = require("./graph");
@@ -10,6 +11,7 @@ const vertex_1 = require("./vertex");
 const r_function_call_1 = require("../../r-bridge/lang-4.x/ast/model/nodes/r-function-call");
 const built_in_1 = require("../environments/built-in");
 const edge_1 = require("./edge");
+const default_builtin_config_1 = require("../environments/default-builtin-config");
 function emptyGraph(idMap) {
     return new DataflowGraphBuilder(idMap);
 }
@@ -244,4 +246,11 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
     }
 }
 exports.DataflowGraphBuilder = DataflowGraphBuilder;
+function getBuiltInSideEffect(name) {
+    const got = default_builtin_config_1.DefaultBuiltinConfig.find(e => e.names.includes(name));
+    if (got?.type !== 'function') {
+        return undefined;
+    }
+    return (got?.config).hasUnknownSideEffects;
+}
 //# sourceMappingURL=dataflowgraph-builder.js.map

package/dataflow/graph/diff.js

@@ -100,7 +100,7 @@ function diffOutgoingEdges(ctx) {
 }
 function diffRootVertices(ctx) {
     (0, diff_1.setDifference)(ctx.left.rootIds(), ctx.right.rootIds(), { ...ctx, position: `${ctx.position}Root vertices differ in graphs. ` });
-    (0, diff_1.setDifference)(ctx.left.unknownSideEffects, ctx.right.unknownSideEffects, { ...ctx, position: `${ctx.position}Unknown side effects differ in graphs. ` });
+    (0, diff_1.setDifference)(new Set([...ctx.left.unknownSideEffects].map(n => typeof n === 'object' ? n.id : n)), new Set([...ctx.right.unknownSideEffects].map(n => typeof n === 'object' ? n.id : n)), { ...ctx, position: `${ctx.position}Unknown side effects differ in graphs. ` });
 }
 function diffOfDataflowGraphs(left, right, config) {
     if (left.graph === right.graph) {

package/dataflow/graph/graph.d.ts

@@ -6,6 +6,7 @@ import { EmptyArgument } from '../../r-bridge/lang-4.x/ast/model/nodes/r-functio
 import type { IdentifierDefinition, IdentifierReference } from '../environments/identifier';
 import type { NodeId } from '../../r-bridge/lang-4.x/ast/model/processing/node-id';
 import type { AstIdMap } from '../../r-bridge/lang-4.x/ast/model/processing/decorate';
+import type { LinkTo } from '../../queries/catalog/call-context-query/call-context-query-format';
 export type DataflowFunctionFlowInformation = Omit<DataflowInformation, 'graph' | 'exitPoints'> & {
     graph: Set<NodeId>;
 };
@@ -45,6 +46,10 @@ export interface DataflowGraphJson {
     readonly vertexInformation: [NodeId, DataflowGraphVertexInfo][];
     readonly edgeInformation: [NodeId, [NodeId, DataflowGraphEdge][]][];
 }
+export type UnknownSidEffect = NodeId | {
+    id: NodeId;
+    linkTo: LinkTo<RegExp>;
+};
 /**
  * The dataflow graph holds the dataflow information found within the given AST.
  * We differentiate the directed edges in {@link EdgeType} and the vertices indicated by {@link DataflowGraphVertexArgument}
@@ -94,7 +99,7 @@ export declare class DataflowGraph<Vertex extends DataflowGraphVertexInfo = Data
     /**
      * Retrieves the set of vertices which have side effects that we do not know anything about.
      */
-    get unknownSideEffects(): ReadonlySet<NodeId>;
+    get unknownSideEffects(): Set<UnknownSidEffect>;
     /** Allows setting the id-map explicitly (which should only be used when, e.g., you plan to compare two dataflow graphs on the same AST-basis) */
     setIdMap(idMap: AstIdMap): void;
     /**
@@ -162,7 +167,7 @@ export declare class DataflowGraph<Vertex extends DataflowGraphVertexInfo = Data
     /** If you do not pass the `to` node, this will just mark the node as maybe */
     addControlDependency(from: NodeId, to?: NodeId, when?: boolean): this;
     /** Marks the given node as having unknown side effects */
-    markIdForUnknownSideEffects(id: NodeId): this;
+    markIdForUnknownSideEffects(id: NodeId, target?: LinkTo<RegExp | string>): this;
     /**
      * Constructs a dataflow graph instance from the given JSON data and returns the result.
      * This can be useful for data sent by the flowR server when analyzing it further.

package/dataflow/graph/graph.js

@@ -47,7 +47,11 @@ function extractEdgeIds(from, to) {
 class DataflowGraph {
     static DEFAULT_ENVIRONMENT = undefined;
     _idMap;
-    /* Set of vertices which have sideEffects that we do not know anything about */
+    /*
+     * Set of vertices which have sideEffects that we do not know anything about.
+     * As a (temporary) solution until we have FD edges, a side effect may also store known target links
+     * that have to be/should be resolved (as globals) as a separate pass before the df analysis ends.
+     */
     _unknownSideEffects = new Set();
     constructor(idMap) {
         DataflowGraph.DEFAULT_ENVIRONMENT ??= (0, environment_1.initializeCleanEnvironments)();
@@ -306,7 +310,11 @@ class DataflowGraph {
         return this;
     }
     /** Marks the given node as having unknown side effects */
-    markIdForUnknownSideEffects(id) {
+    markIdForUnknownSideEffects(id, target) {
+        if (target) {
+            this._unknownSideEffects.add({ id: (0, node_id_1.normalizeIdToNumberIfPossible)(id), linkTo: typeof target.callName === 'string' ? { ...target, callName: new RegExp(target.callName) } : target });
+            return this;
+        }
         this._unknownSideEffects.add((0, node_id_1.normalizeIdToNumberIfPossible)(id));
         return this;
     }

package/dataflow/internal/process/functions/call/argument/unpack-argument.d.ts

@@ -1,3 +1,3 @@
 import type { RFunctionArgument } from '../../../../../../r-bridge/lang-4.x/ast/model/nodes/r-function-call';
 import type { RNode } from '../../../../../../r-bridge/lang-4.x/ast/model/model';
-export declare function unpackArgument<OtherInfo>(arg: RFunctionArgument<OtherInfo>): RNode<OtherInfo> | undefined;
+export declare function unpackArgument<OtherInfo>(arg: RFunctionArgument<OtherInfo>, noNameOnly?: boolean): RNode<OtherInfo> | undefined;

package/dataflow/internal/process/functions/call/argument/unpack-argument.js

@@ -3,12 +3,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.unpackArgument = unpackArgument;
 const log_1 = require("../../../../../../util/log");
 const r_function_call_1 = require("../../../../../../r-bridge/lang-4.x/ast/model/nodes/r-function-call");
-function unpackArgument(arg) {
+function unpackArgument(arg, noNameOnly = true) {
     if (arg === r_function_call_1.EmptyArgument) {
         log_1.log.trace('Argument is empty, skipping');
         return undefined;
     }
-    else if (arg.name !== undefined) {
+    else if (noNameOnly && arg.name !== undefined) {
         log_1.log.trace(`Argument ${JSON.stringify(arg)} is not unnamed, skipping`);
         return undefined;
     }

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

@@ -111,8 +111,8 @@ args, rootId, data, config) {
     return (0, known_call_handling_1.processKnownFunctionCall)({ name, args: effectiveArgs, rootId, data, forceArgs: config.forceArgs }).information;
 }
 function extractSourceAndTarget(args, name) {
-    const source = (0, unpack_argument_1.unpackArgument)(args[1]);
-    const target = (0, unpack_argument_1.unpackArgument)(args[0]);
+    const source = (0, unpack_argument_1.unpackArgument)(args[1], false);
+    const target = (0, unpack_argument_1.unpackArgument)(args[0], false);
     (0, assert_1.guard)(source !== undefined, () => `Assignment ${name.content} has no source, impossible!`);
     (0, assert_1.guard)(target !== undefined, () => `Assignment ${name.content} has no target, impossible!`);
     return { source, target };

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

@@ -82,7 +82,7 @@ function updateSideEffectsForCalledFunctions(calledEnvs, inputEnvironment, nextG
     return inputEnvironment;
 }
 function processExpressionList(name, args, rootId, data) {
-    const expressions = args.map(unpack_argument_1.unpackArgument);
+    const expressions = args.map(e => (0, unpack_argument_1.unpackArgument)(e));
     logger_1.dataflowLogger.trace(() => `[expr list] with ${expressions.length} expressions`);
     let { environment } = data;
     // used to detect if a "write" happens within the same expression list

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

@@ -20,7 +20,7 @@ function processForLoop(name, args, rootId, data) {
         logger_1.dataflowLogger.warn(`For-Loop ${name.content} does not have three arguments, skipping`);
         return (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data }).information;
     }
-    const [variableArg, vectorArg, bodyArg] = args.map(unpack_argument_1.unpackArgument);
+    const [variableArg, vectorArg, bodyArg] = args.map(e => (0, unpack_argument_1.unpackArgument)(e));
     (0, assert_1.guard)(variableArg !== undefined && vectorArg !== undefined && bodyArg !== undefined, () => `For-Loop ${JSON.stringify(args)} has missing arguments! Bad!`);
     const vector = (0, processor_1.processDataflowFor)(vectorArg, data);
     if ((0, info_1.alwaysExits)(vector)) {

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

@@ -17,7 +17,7 @@ function processIfThenElse(name, args, rootId, data) {
         logger_1.dataflowLogger.warn(`If-then-else ${name.content} has something different from 2 or 3 arguments, skipping`);
         return (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data }).information;
     }
-    const [condArg, thenArg, otherwiseArg] = args.map(unpack_argument_1.unpackArgument);
+    const [condArg, thenArg, otherwiseArg] = args.map(e => (0, unpack_argument_1.unpackArgument)(e));
     if (condArg === undefined || thenArg === undefined) {
         logger_1.dataflowLogger.warn(`If-then-else ${name.content} has empty condition or then case in ${JSON.stringify(args)}, skipping`);
         return (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data }).information;

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

@@ -15,7 +15,7 @@ function processPipe(name, args, rootId, data) {
         logger_1.dataflowLogger.warn(`Pipe ${name.content} has something else than 2 arguments, skipping`);
         return information;
     }
-    const [lhs, rhs] = args.map(unpack_argument_1.unpackArgument);
+    const [lhs, rhs] = args.map(e => (0, unpack_argument_1.unpackArgument)(e));
     (0, assert_1.guard)(lhs !== undefined && rhs !== undefined, () => `lhs and rhs must be present, but ${JSON.stringify(lhs)} and ${JSON.stringify(rhs)} were found instead.`);
     if (rhs.type !== type_1.RType.FunctionCall) {
         logger_1.dataflowLogger.warn(`Expected rhs of pipe to be a function call, but got ${rhs.type} instead.`);

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

@@ -1,4 +1,7 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.setSourceProvider = setSourceProvider;
 exports.processSourceCall = processSourceCall;
@@ -17,6 +20,7 @@ const logger_1 = require("../../../../../logger");
 const type_1 = require("../../../../../../r-bridge/lang-4.x/ast/model/type");
 const overwrite_1 = require("../../../../../environments/overwrite");
 const log_1 = require("../../../../../../util/log");
+const fs_1 = __importDefault(require("fs"));
 let sourceProvider = (0, retriever_1.requestProviderFromFile)();
 function setSourceProvider(provider) {
     sourceProvider = provider;
@@ -49,13 +53,21 @@ function processSourceCall(name, args, rootId, data, config) {
     }
 }
 function sourceRequest(rootId, request, data, information, getId) {
+    if (request.request === 'file') {
+        /* 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);
+            return information;
+        }
+    }
     const executor = new shell_executor_1.RShellExecutor();
     // parse, normalize and dataflow the sourced file
     let normalized;
     let dataflow;
     try {
         const parsed = (0, retriever_1.retrieveParseDataFromRCode)(request, executor);
-        normalized = (0, parser_1.normalize)(parsed, getId);
+        normalized = (0, parser_1.normalize)({ parsed }, getId);
         dataflow = (0, processor_1.processDataflowFor)(normalized.ast, {
             ...data,
             currentRequest: request,

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

@@ -16,7 +16,7 @@ function processWhileLoop(name, args, rootId, data) {
         logger_1.dataflowLogger.warn(`While-Loop ${name.content} does not have 2 arguments, skipping`);
         return (0, known_call_handling_1.processKnownFunctionCall)({ name, args, rootId, data }).information;
     }
-    const unpackedArgs = args.map(unpack_argument_1.unpackArgument);
+    const unpackedArgs = args.map(e => (0, unpack_argument_1.unpackArgument)(e));
     if (unpackedArgs.some(assert_1.isUndefined)) {
         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 }).information;

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

@@ -33,7 +33,7 @@ function processNamedCall(name, args, rootId, data) {
     let information = undefined;
     let builtIn = false;
     for (const resolvedFunction of resolved) {
-        if (resolvedFunction.type === identifier_1.ReferenceType.BuiltInFunction) {
+        if (resolvedFunction.type === identifier_1.ReferenceType.BuiltInFunction && typeof resolvedFunction.processor === 'function') {
             builtIn = true;
             information = mergeInformation(information, resolvedFunction.processor(name, args, rootId, data));
         }

package/dataflow/processor.d.ts

@@ -8,8 +8,8 @@ import type { RParseRequest } from '../r-bridge/retriever';
 import type { RNode } from '../r-bridge/lang-4.x/ast/model/model';
 export interface DataflowProcessorInformation<OtherInfo> {
     /**
-   * Initial and frozen ast-information
-   */
+    * Initial and frozen ast-information
+    */
     readonly completeAst: NormalizedAst<OtherInfo>;
     /**
    * Correctly contains pushed local scopes introduced by `function` scopes.
@@ -30,7 +30,7 @@ export interface DataflowProcessorInformation<OtherInfo> {
      */
     readonly referenceChain: string[];
     /**
-     * The chain of control-flow {@link NodeId}s that lead to the current node (e.g. of known ifs).
+     * The chain of control-flow {@link NodeId}s that lead to the current node (e.g., of known ifs).
      */
     readonly controlDependencies: ControlDependency[] | undefined;
 }

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

@@ -16,9 +16,8 @@ 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/catalog/call-context-query/call-context-query-format");
 const message_lineage_1 = require("../../../cli/repl/server/messages/message-lineage");
-const doc_structure_1 = require("../../doc-util/doc-structure");
+const identify_link_to_last_call_relation_1 = require("../../../queries/catalog/call-context-query/identify-link-to-last-call-relation");
 function documentAllServerMessages() {
     (0, doc_server_message_1.documentServerMessage)({
         title: 'Hello',
@@ -202,6 +201,7 @@ While the context is derived from the \`filename\`, we currently offer no way to
 	`;
         }
     });
+    const deprecatedByQuery = `(<a href="${doc_files_1.FlowrWikiBaseRef}/Query%20API">deprecated</a>)`;
     (0, doc_server_message_1.documentServerMessage)({
         title: 'Slice',
         type: 'request',
@@ -218,13 +218,10 @@ While the context is derived from the \`filename\`, we currently offer no way to
     end
     deactivate  Server
 	`,
-        shortDescription: `([DEPRECATED](${doc_files_1.FlowrWikiBaseRef}/Query%20API)) The server slices a file based on the given criteria.`,
+        shortDescription: `${deprecatedByQuery} The server slices a file based on the given criteria.`,
         text: async (shell) => {
             return `
-${(0, doc_structure_1.block)({
-                type: 'WARNING',
-                content: `We deprecated the slice request in favor of the \`static-slice\` [Query](${doc_files_1.FlowrWikiBaseRef}/Query%20API).`
-            })}
+**We deprecated the slice request in favor of the \`static-slice\` [Query](${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](${doc_files_1.FlowrWikiBaseRef}/Terminology#slicing-criterion) 
@@ -427,7 +424,7 @@ See [above](#message-request-file-analysis) for the general structure of the res
                                     commonArguments: {
                                         kind: 'visualize',
                                         subkind: 'text',
-                                        callTargets: call_context_query_format_1.CallTargets.OnlyGlobal,
+                                        callTargets: identify_link_to_last_call_relation_1.CallTargets.OnlyGlobal,
                                     },
                                     arguments: [
                                         {
@@ -435,7 +432,7 @@ See [above](#message-request-file-analysis) for the general structure of the res
                                         },
                                         {
                                             callName: '^print$',
-                                            callTargets: call_context_query_format_1.CallTargets.OnlyLocal
+                                            callTargets: identify_link_to_last_call_relation_1.CallTargets.OnlyLocal
                                         }
                                     ]
                                 }
@@ -467,14 +464,11 @@ See [above](#message-request-file-analysis) for the general structure of the res
     end
     deactivate  Server
 	`,
-        shortDescription: '([DEPRECATED](${FlowrWikiBaseRef}/Query%20API)) Obtain the lineage of a given slicing criterion.',
+        shortDescription: `${deprecatedByQuery} Obtain the lineage of a given slicing criterion.`,
         text: async (shell) => {
             return `
 
-${(0, doc_structure_1.block)({
-                type: 'WARNING',
-                content: `We deprecated the lineage request in favor of the \`lineage\` [Query](${doc_files_1.FlowrWikiBaseRef}/Query%20API).`
-            })}
+**We deprecated the lineage request in favor of the \`lineage\` [Query](${doc_files_1.FlowrWikiBaseRef}/Query%20API).**
 
 In order to retrieve the lineage of an object, 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 retrieve the lineage of the same file.
 Besides that, you will need to add a [criterion](${doc_files_1.FlowrWikiBaseRef}/Terminology#slicing-criterion) that specifies the object whose lineage you're interested in.

package/documentation/doc-util/doc-cli-option.js

@@ -6,7 +6,7 @@ exports.getReplCommand = getReplCommand;
 /** Automatically provides hover over with the documentation for these! */
 const scripts_info_1 = require("../../cli/common/scripts-info");
 const assert_1 = require("../../util/assert");
-const doc_hover_over_1 = require("./doc-hover-over");
+const html_hover_over_1 = require("../../util/html-hover-over");
 const flowr_main_options_1 = require("../../cli/flowr-main-options");
 const repl_commands_1 = require("../../cli/repl/commands/repl-commands");
 function getCliLongOptionOf(scriptName, optionName, withAlias = false, quote = true) {
@@ -15,10 +15,10 @@ function getCliLongOptionOf(scriptName, optionName, withAlias = false, quote = t
     const option = script.find(({ name }) => name === optionName);
     (0, assert_1.guard)(option !== undefined, () => `Unknown option ${optionName}, pick one of ${JSON.stringify(script.map(o => o.name))}.`);
     const char = quote ? '`' : '';
-    const alias = withAlias && option.alias ? ' (alias:' + (0, doc_hover_over_1.textWithTooltip)(`${char}-${option.alias}${char}`, option.description) + ')' : '';
+    const alias = withAlias && option.alias ? ' (alias:' + (0, html_hover_over_1.textWithTooltip)(`${char}-${option.alias}${char}`, option.description) + ')' : '';
     const ligatureBreaker = quote ? '' : '<span/>';
     // span ensures split even with ligatures
-    return (0, doc_hover_over_1.textWithTooltip)(`${char}-${ligatureBreaker}-${optionName}${char}`, 'Description (Command Line Argument): ' + option.description) + alias;
+    return (0, html_hover_over_1.textWithTooltip)(`${char}-${ligatureBreaker}-${optionName}${char}`, 'Description (Command Line Argument): ' + option.description) + alias;
 }
 function multipleCliOptions(scriptName, ...options) {
     return options.map(o => getCliLongOptionOf(scriptName, o, false, true)).join(' ');
@@ -31,6 +31,6 @@ function getReplCommand(commandName, quote = true, showStar = false) {
     const aliases = commands.aliases.length > 0 ? ' (aliases: ' + commands.aliases.map(a => `:${a}`).join(', ') + ')' : '';
     const starredComment = commandName.endsWith('*') ? ', starred version' : '';
     const baseDescription = commandName.endsWith('*') ? '; Base Command: ' + availableNames[commandName.slice(0, -1)].description : '';
-    return (0, doc_hover_over_1.textWithTooltip)(`${char}:${commandName}${showStar ? '[*]' : ''}${char}`, `Description (Repl Command${starredComment}): ` + commands.description + baseDescription + aliases);
+    return (0, html_hover_over_1.textWithTooltip)(`${char}:${commandName}${showStar ? '[*]' : ''}${char}`, `Description (Repl Command${starredComment}): ` + commands.description + baseDescription + aliases);
 }
 //# sourceMappingURL=doc-cli-option.js.map

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

@@ -1,16 +1,13 @@
 import type { RShell } from '../../r-bridge/shell';
-import type { Queries, QueryResults, SupportedQueryTypes } from '../../queries/query';
-import { DEFAULT_DATAFLOW_PIPELINE } from '../../core/steps/pipeline/default-pipelines';
-import { type OutputFormatter } from '../../util/ansi';
+import type { Queries, SupportedQueryTypes } from '../../queries/query';
 import type { SupportedVirtualQueryTypes } from '../../queries/virtual-query/virtual-queries';
 import type { VirtualCompoundConstraint } from '../../queries/virtual-query/compound-query';
-import type { PipelineOutput } from '../../core/steps/pipeline/pipeline';
 export interface ShowQueryOptions {
     readonly showCode?: boolean;
     readonly collapseResult?: boolean;
+    readonly collapseQuery?: boolean;
 }
-export declare function asciiSummaryOfQueryResult(formatter: OutputFormatter, totalInMs: number, results: QueryResults<SupportedQueryTypes>, processed: 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 }?: 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 }?: ShowQueryOptions): Promise<string>;
 export interface QueryDocumentation {
     readonly name: string;
     readonly type: 'virtual' | 'active';
@@ -24,5 +21,6 @@ export declare const RegisteredQueries: {
     virtual: Map<string, QueryDocumentation>;
 };
 export declare function registerQueryDocumentation(query: SupportedQueryTypes | SupportedVirtualQueryTypes, doc: QueryDocumentation): void;
+export declare function linkToQueryOfName(id: SupportedQueryTypes | SupportedVirtualQueryTypes): string;
 export declare function tocForQueryType(type: 'active' | 'virtual'): string;
 export declare function explainQueries(shell: RShell, type: 'active' | 'virtual'): Promise<string>;