[Query API] Script dependencies

src/cli/repl/commands/repl-query.ts

@@ -7,12 +7,12 @@ import { splitAtEscapeSensitive } from '../../../util/args';
 import { italic } from '../../../util/ansi';
 import { describeSchema } from '../../../util/schema';
 import type { Query, QueryResults, SupportedQueryTypes } from '../../../queries/query';
-import {  executeQueries } from '../../../queries/query';
-
+import { executeQueries } from '../../../queries/query';
 import type { PipelineOutput } from '../../../core/steps/pipeline/pipeline';
 import { jsonReplacer } from '../../../util/json';
 import { AnyQuerySchema, QueriesSchema } from '../../../queries/query-schema';
 
+
 async function getDataflow(shell: RShell, remainingLine: string) {
 	return await new PipelineExecutor(DEFAULT_DATAFLOW_PIPELINE, {
 		shell,

src/dataflow/internal/process/functions/call/built-in/built-in-source.ts

@@ -25,6 +25,7 @@ import { RType } from '../../../../../../r-bridge/lang-4.x/ast/model/type';
 import { overwriteEnvironment } from '../../../../../environments/overwrite';
 import type { NoInfo } from '../../../../../../r-bridge/lang-4.x/ast/model/model';
 import { expensiveTrace } from '../../../../../../util/log';
+import fs from 'fs';
 
 let sourceProvider = requestProviderFromFile();
 
@@ -76,6 +77,14 @@ export function processSourceCall<OtherInfo>(
 }
 
 export function sourceRequest<OtherInfo>(rootId: NodeId, request: RParseRequest, data: DataflowProcessorInformation<OtherInfo & ParentInformation>, information: DataflowInformation, getId: IdGenerator<NoInfo>): DataflowInformation {
+	if(request.request === 'file') {
+		/* check if the file exists and if not, fail */
+		if(!fs.existsSync(request.content)) {
+			dataflowLogger.warn(`Failed to analyze sourced file ${JSON.stringify(request)}: file does not exist`);
+			information.graph.markIdForUnknownSideEffects(rootId);
+			return information;
+		}
+	}
 	const executor = new RShellExecutor();
 
 	// parse, normalize and dataflow the sourced file

src/documentation/doc-util/doc-query.ts

@@ -1,7 +1,6 @@
 import type { RShell } from '../../r-bridge/shell';
 import type { Queries, QueryResults, SupportedQueryTypes } from '../../queries/query';
 import { SupportedQueries , executeQueries } from '../../queries/query';
-
 import { PipelineExecutor } from '../../core/pipeline-executor';
 import { DEFAULT_DATAFLOW_PIPELINE } from '../../core/steps/pipeline/default-pipelines';
 import { requestFromInput } from '../../r-bridge/retriever';

src/queries/catalog/dependencies-query/dependencies-query-executor.ts

@@ -0,0 +1,128 @@
+import type { BasicQueryData } from '../../query';
+import { executeQueries } from '../../query';
+import type {
+	DependenciesQuery,
+	DependenciesQueryResult, DependencyInfo,
+	FunctionInfo,
+	LibraryInfo,
+	ReadInfo, SourceInfo,
+	WriteInfo
+} from './dependencies-query-format';
+import { LibraryFunctions, ReadFunctions, SourceFunctions, WriteFunctions } from './dependencies-query-format';
+import type { CallContextQuery, CallContextQueryResult } from '../call-context-query/call-context-query-format';
+import type { DataflowGraphVertexFunctionCall } from '../../../dataflow/graph/vertex';
+import { getReferenceOfArgument } from '../../../dataflow/graph/graph';
+import { log } from '../../../util/log';
+import { RType } from '../../../r-bridge/lang-4.x/ast/model/type';
+import { removeRQuotes } from '../../../r-bridge/retriever';
+import { EmptyArgument } from '../../../r-bridge/lang-4.x/ast/model/nodes/r-function-call';
+import type { NodeId } from '../../../r-bridge/lang-4.x/ast/model/processing/node-id';
+
+const SupportedVertexTypes = [RType.String, RType.Logical, RType.Number];
+
+const Unknown = 'unknown';
+
+export function executeDependenciesQuery(data: BasicQueryData, queries: readonly DependenciesQuery[]): DependenciesQueryResult {
+	if(queries.length !== 1) {
+		log.warn('Dependencies query expects only up to one query, but got ', queries.length);
+	}
+	const now = Date.now();
+
+	const query = queries[0];
+	const ignoreDefault = query.ignoreDefaultFunctions ?? false;
+	const libraryFunctions = getFunctionsToCheck(query.libraryFunctions, ignoreDefault, LibraryFunctions);
+	const sourceFunctions = getFunctionsToCheck(query.sourceFunctions, ignoreDefault, SourceFunctions);
+	const readFunctions = getFunctionsToCheck(query.readFunctions, ignoreDefault, ReadFunctions);
+	const writeFunctions = getFunctionsToCheck(query.writeFunctions, ignoreDefault, WriteFunctions);
+
+	const results = executeQueries(data, [
+		...makeCallContextQuery(libraryFunctions, 'library'),
+		...makeCallContextQuery(sourceFunctions, 'source'),
+		...makeCallContextQuery(readFunctions, 'read'),
+		...makeCallContextQuery(writeFunctions, 'write')
+	])['call-context'];
+
+	const libraries: LibraryInfo[] = getResults(data, results, 'library', libraryFunctions, (id, vertex, argument) => ({
+		nodeId:       id,
+		functionName: vertex.name,
+		libraryName:  argument ?? Unknown
+	}), [RType.Symbol]);
+	const sourcedFiles: SourceInfo[] = getResults(data, results, 'source', sourceFunctions, (id, vertex, argument) => ({
+		nodeId:       id,
+		functionName: vertex.name,
+		file:         argument ?? Unknown
+	}));
+	const readData: ReadInfo[] = getResults(data, results, 'read', readFunctions, (id, vertex, argument) => ({
+		nodeId:       id,
+		functionName: vertex.name,
+		source:       argument ?? Unknown
+	}));
+	const writtenData: WriteInfo[] = getResults(data, results, 'write', writeFunctions, (id, vertex, argument) => ({
+		nodeId:       id,
+		functionName: vertex.name,
+		// write functions that don't have argIndex are assumed to write to stdout
+		destination:  argument ?? 'stdout'
+	}));
+
+	return {
+		'.meta': {
+			timing: Date.now() - now
+		},
+		libraries, sourcedFiles, readData, writtenData
+	};
+}
+
+function makeCallContextQuery(functions: readonly FunctionInfo[], kind: string): CallContextQuery[] {
+	return functions.map(f => ({
+		type:           'call-context',
+		callName:       f.name,
+		includeAliases: true,
+		callNameExact:  true,
+		subkind:        f.name,
+		kind
+	}));
+}
+
+function getResults<T extends DependencyInfo>(data: BasicQueryData, results: CallContextQueryResult, kind: string, functions: FunctionInfo[], makeInfo: (id: NodeId, vertex: DataflowGraphVertexFunctionCall, argument: string | undefined) => T | undefined, additionalAllowedTypes?: RType[]) {
+	return Object.entries(results?.kinds[kind]?.subkinds ?? {}).flatMap(([name, results]) => results.map(({ id }) => {
+		const vertex = data.graph.getVertex(id) as DataflowGraphVertexFunctionCall;
+		const info = functions.find(f => f.name === name) as FunctionInfo;
+		let index = info.argIdx;
+		if(info.argName) {
+			const arg = vertex?.args.findIndex(arg => arg !== EmptyArgument && arg.name === info.argName);
+			if(arg >= 0) {
+				index = arg;
+			}
+		}
+		const argument = index !== undefined ? getArgumentValue(data, vertex, index, additionalAllowedTypes) : undefined;
+		return makeInfo(id, vertex, argument);
+	})).filter(x => x !== undefined) ?? [];
+}
+
+function getArgumentValue({ graph }: BasicQueryData, vertex: DataflowGraphVertexFunctionCall, argumentIndex: number, additionalAllowedTypes: RType[] | undefined): string | undefined {
+	if(vertex && vertex.args.length > argumentIndex) {
+		const arg = getReferenceOfArgument(vertex.args[argumentIndex]);
+		if(arg) {
+			let valueNode = graph.idMap?.get(arg);
+			if(valueNode?.type === RType.Argument) {
+				valueNode = valueNode.value;
+			}
+			if(valueNode) {
+				const allowedTypes = [...SupportedVertexTypes, ...additionalAllowedTypes ?? []];
+				return allowedTypes.includes(valueNode.type) ? removeRQuotes(valueNode.lexeme as string) : Unknown;
+			}
+		}
+	}
+	return undefined;
+}
+
+function getFunctionsToCheck(customFunctions: FunctionInfo[] | undefined, ignoreDefaultFunctions: boolean, defaultFunctions: FunctionInfo[]): FunctionInfo[] {
+	const functions: FunctionInfo[] = [];
+	if(!ignoreDefaultFunctions) {
+		functions.push(...defaultFunctions);
+	}
+	if(customFunctions) {
+		functions.push(...customFunctions);
+	}
+	return functions;
+}

src/queries/catalog/dependencies-query/dependencies-query-format.ts

@@ -0,0 +1,129 @@
+import type { BaseQueryFormat, BaseQueryResult } from '../../base-query-format';
+import type { NodeId } from '../../../r-bridge/lang-4.x/ast/model/processing/node-id';
+import type { QueryResults, SupportedQuery } from '../../query';
+import { bold } from '../../../util/ansi';
+import { printAsMs } from '../../../util/time';
+import Joi from 'joi';
+import { executeDependenciesQuery } from './dependencies-query-executor';
+
+// these lists are originally based on https://github.com/duncantl/CodeDepends/blob/7fd96dfee16b252e5f642c77a7ababf48e9326f8/R/codeTypes.R
+export const LibraryFunctions: FunctionInfo[] = [
+	{ name: 'library',         argIdx: 0, argName: 'package' },
+	{ name: 'require',         argIdx: 0, argName: 'package' },
+	{ name: 'loadNamespace',   argIdx: 0, argName: 'package' },
+	{ name: 'attachNamespace', argIdx: 0, argName: 'ns' },
+] as const;
+export const SourceFunctions: FunctionInfo[] = [
+	{ name: 'source', argIdx: 0, argName: 'file' }
+] as const;
+export const ReadFunctions: FunctionInfo[] = [
+	{ name: 'read.table', argIdx: 0, argName: 'file' },
+	{ name: 'read.csv', argIdx: 0, argName: 'file' },
+	{ name: 'read.csv2', argIdx: 0, argName: 'file' },
+	{ name: 'read.delim', argIdx: 0, argName: 'file' },
+	{ name: 'read.delim', argIdx: 0, argName: 'file' },
+	{ name: 'read.fwf', argIdx: 0, argName: 'file' },
+	{ name: 'file', argIdx: 1, argName: 'open' },
+	{ name: 'url', argIdx: 1, argName: 'open' },
+	{ name: 'load', argIdx: 0, argName: 'file' },
+	{ name: 'gzfile', argIdx: 1, argName: 'open' },
+	{ name: 'bzfile', argIdx: 1, argName: 'open' },
+	{ name: 'download.file', argIdx: 0, argName: 'url' },
+	{ name: 'pipe', argIdx: 1, argName: 'open' },
+	{ name: 'fifo', argIdx: 1, argName: 'open' },
+	{ name: 'unz', argIdx: 1, argName: 'open' },
+	{ name: 'matrix', argIdx: 0, argName: 'data' },
+	{ name: 'readRDS', argIdx: 0, argName: 'file' },
+	{ name: 'readLines', argIdx: 0, argName: 'con' },
+] as const;
+export const WriteFunctions: FunctionInfo[] = [
+	{ name: 'save', argIdx: 0, argName: '...' },
+	{ name: 'save.image', argIdx: 0, argName: 'file' },
+	{ name: 'write', argIdx: 1, argName: 'file' },
+	{ name: 'dput', argIdx: 1, argName: 'file' },
+	{ name: 'dump', argIdx: 1, argName: 'file' },
+	{ name: 'write.table', argIdx: 1, argName: 'file' },
+	{ name: 'write.csv', argIdx: 1, argName: 'file' },
+	{ name: 'saveRDS', argIdx: 1, argName: 'file' },
+	// write functions that don't have argIndex are assumed to write to stdout
+	{ name: 'print' },
+	{ name: 'cat' },
+] as const;
+
+export interface FunctionInfo {
+    name:     string
+    argIdx?:  number
+    argName?: string
+}
+
+export interface DependenciesQuery extends BaseQueryFormat {
+    readonly type:                    'dependencies'
+    readonly ignoreDefaultFunctions?: boolean
+    readonly libraryFunctions?:       FunctionInfo[]
+    readonly sourceFunctions?:        FunctionInfo[]
+    readonly readFunctions?:          FunctionInfo[]
+    readonly writeFunctions?:         FunctionInfo[]
+}
+
+export interface DependenciesQueryResult extends BaseQueryResult {
+    libraries:    LibraryInfo[]
+    sourcedFiles: SourceInfo[]
+    readData:     ReadInfo[]
+    writtenData:  WriteInfo[]
+}
+
+export interface DependencyInfo {
+    nodeId:       NodeId
+    functionName: string
+}
+export type LibraryInfo = (DependencyInfo & { libraryName: 'unknown' | string })
+export type SourceInfo = (DependencyInfo & { file: string })
+export type ReadInfo = (DependencyInfo & { source: string })
+export type WriteInfo = (DependencyInfo & { destination: 'stdout' | string })
+
+function printResultSection<T extends DependencyInfo>(title: string, infos: T[], result: string[], sectionSpecifics: (info: T) => string): void {
+	if(infos.length <= 0) {
+		return;
+	}
+	result.push(`   ╰ ${title}`);
+	const grouped = infos.reduce(function(groups: Map<string, T[]>, i) {
+		const array = groups.get(i.functionName);
+		if(array) {
+			array.push(i);
+		} else {
+			groups.set(i.functionName, [i]);
+		}
+		return groups;
+	}, new Map<string, T[]>());
+	for(const [functionName, infos] of grouped) {
+		result.push(`       ╰ ${functionName}`);
+		result.push(infos.map(i => `           ╰ Node Id: ${i.nodeId}, ${sectionSpecifics(i)}`).join('\n'));
+	}
+}
+
+const functionInfoSchema: Joi.ArraySchema = Joi.array().items(Joi.object({
+	name:    Joi.string().required().description('The name of the library function.'),
+	argIdx:  Joi.number().optional().description('The index of the argument that contains the library name.'),
+	argName: Joi.string().optional().description('The name of the argument that contains the library name.'),
+})).optional();
+
+export const DependenciesQueryDefinition = {
+	executor:        executeDependenciesQuery,
+	asciiSummarizer: (formatter, _processed, queryResults, result) => {
+		const out = queryResults as QueryResults<'dependencies'>['dependencies'];
+		result.push(`Query: ${bold('dependencies', formatter)} (${printAsMs(out['.meta'].timing, 0)})`);
+		printResultSection('Libraries', out.libraries, result, l => `Library Name: ${l.libraryName}`);
+		printResultSection('Sourced Files', out.sourcedFiles, result, s => `Sourced File: ${s.file}`);
+		printResultSection('Read Data', out.readData, result, r => `Source: ${r.source}`);
+		printResultSection('Written Data', out.writtenData, result, w => `Destination: ${w.destination}`);
+		return true;
+	},
+	schema: Joi.object({
+		type:                   Joi.string().valid('dependencies').required().description('The type of the query.'),
+		ignoreDefaultFunctions: Joi.boolean().optional().description('Should the set of functions that are detected by default be ignored/skipped?'),
+		libraryFunctions:       functionInfoSchema.description('The set of library functions to search for.'),
+		sourceFunctions:        functionInfoSchema.description('The set of source functions to search for.'),
+		readFunctions:          functionInfoSchema.description('The set of data reading functions to search for.'),
+		writeFunctions:         functionInfoSchema.description('The set of data writing functions to search for.'),
+	}).description('The dependencies query retrieves and returns the set of all dependencies in the dataflow graph, which includes libraries, sourced files, read data, and written data.')
+} as const satisfies SupportedQuery<'dependencies'>;

src/queries/catalog/lineage-query/lineage-query-format.ts

@@ -32,7 +32,7 @@ export const LineageQueryDefinition = {
 		return true;
 	},
 	schema: Joi.object({
-		type: Joi.string().valid('lineage').required().description('The type of the query.'),
-		id:   Joi.string().required().description('The ID of the node to get the lineage of.')
+		type:      Joi.string().valid('lineage').required().description('The type of the query.'),
+		criterion: Joi.string().required().description('The slicing criterion of the node to get the lineage of.')
 	}).description('Lineage query used to find the lineage of a node in the dataflow graph')
 } as const satisfies SupportedQuery<'lineage'>;

src/queries/query.ts

@@ -1,6 +1,7 @@
-import type { CallContextQuery } from './catalog/call-context-query/call-context-query-format';
+import type {
+	CallContextQuery
+} from './catalog/call-context-query/call-context-query-format';
 import { CallContextQueryDefinition } from './catalog/call-context-query/call-context-query-format';
-
 import type { DataflowGraph } from '../dataflow/graph/graph';
 import type { BaseQueryFormat, BaseQueryResult } from './base-query-format';
 import { guard } from '../util/assert';
@@ -15,18 +16,20 @@ import type { IdMapQuery } from './catalog/id-map-query/id-map-query-format';
 import { IdMapQueryDefinition } from './catalog/id-map-query/id-map-query-format';
 import type { NormalizedAstQuery } from './catalog/normalized-ast-query/normalized-ast-query-format';
 import { NormalizedAstQueryDefinition } from './catalog/normalized-ast-query/normalized-ast-query-format';
-import type { DataflowClusterQuery } from './catalog/cluster-query/cluster-query-format';
-import { ClusterQueryDefinition } from './catalog/cluster-query/cluster-query-format';
-import type { StaticSliceQuery } from './catalog/static-slice-query/static-slice-query-format';
-import { StaticSliceQueryDefinition } from './catalog/static-slice-query/static-slice-query-format';
 import type { LineageQuery } from './catalog/lineage-query/lineage-query-format';
 import { LineageQueryDefinition } from './catalog/lineage-query/lineage-query-format';
-import { type OutputFormatter } from '../util/ansi';
+import type { StaticSliceQuery } from './catalog/static-slice-query/static-slice-query-format';
+import { StaticSliceQueryDefinition } from './catalog/static-slice-query/static-slice-query-format';
+import type { DataflowClusterQuery } from './catalog/cluster-query/cluster-query-format';
+import { ClusterQueryDefinition } from './catalog/cluster-query/cluster-query-format';
+import type { DependenciesQuery } from './catalog/dependencies-query/dependencies-query-format';
+import { DependenciesQueryDefinition } from './catalog/dependencies-query/dependencies-query-format';
+import type { OutputFormatter } from '../util/ansi';
 import type { PipelineOutput } from '../core/steps/pipeline/pipeline';
 import type { DEFAULT_DATAFLOW_PIPELINE } from '../core/steps/pipeline/default-pipelines';
 import type Joi from 'joi';
 
-export type Query = CallContextQuery | DataflowQuery | NormalizedAstQuery | IdMapQuery | DataflowClusterQuery | StaticSliceQuery | LineageQuery;
+export type Query = CallContextQuery | DataflowQuery | NormalizedAstQuery | IdMapQuery | DataflowClusterQuery | StaticSliceQuery | LineageQuery | DependenciesQuery;
 
 export type QueryArgumentsWithType<QueryType extends BaseQueryFormat['type']> = Query & { type: QueryType };
 
@@ -55,7 +58,8 @@ export const SupportedQueries = {
 	'normalized-ast':   NormalizedAstQueryDefinition,
 	'dataflow-cluster': ClusterQueryDefinition,
 	'static-slice':     StaticSliceQueryDefinition,
-	'lineage':          LineageQueryDefinition
+	'lineage':          LineageQueryDefinition,
+	'dependencies':     DependenciesQueryDefinition
 } as const satisfies SupportedQueries;
 
 export type SupportedQueryTypes = keyof typeof SupportedQueries;