@eagleoutice/flowr 2.2.10 → 2.2.12

package/queries/catalog/dependencies-query/dependencies-query-executor.js

@@ -12,6 +12,11 @@ const visitor_1 = require("../../../r-bridge/lang-4.x/ast/model/processing/visit
 const assert_1 = require("../../../util/assert");
 const objects_1 = require("../../../util/objects");
 const resolve_by_name_1 = require("../../../dataflow/environments/resolve-by-name");
+const library_functions_1 = require("./function-info/library-functions");
+const source_functions_1 = require("./function-info/source-functions");
+const read_functions_1 = require("./function-info/read-functions");
+const write_functions_1 = require("./function-info/write-functions");
+const function_info_1 = require("./function-info/function-info");
 function collectNamespaceAccesses(data, libraries) {
     /* for libraries, we have to additionally track all uses of `::` and `:::`, for this we currently simply traverse all uses */
     (0, visitor_1.visitAst)(data.ast.ast, n => {
@@ -32,10 +37,10 @@ function executeDependenciesQuery(data, queries) {
     const now = Date.now();
     const [query] = queries;
     const ignoreDefault = query.ignoreDefaultFunctions ?? false;
-    const libraryFunctions = getFunctionsToCheck(query.libraryFunctions, ignoreDefault, dependencies_query_format_1.LibraryFunctions);
-    const sourceFunctions = getFunctionsToCheck(query.sourceFunctions, ignoreDefault, dependencies_query_format_1.SourceFunctions);
-    const readFunctions = getFunctionsToCheck(query.readFunctions, ignoreDefault, dependencies_query_format_1.ReadFunctions);
-    const writeFunctions = getFunctionsToCheck(query.writeFunctions, ignoreDefault, dependencies_query_format_1.WriteFunctions);
+    const libraryFunctions = getFunctionsToCheck(query.libraryFunctions, ignoreDefault, library_functions_1.LibraryFunctions);
+    const sourceFunctions = getFunctionsToCheck(query.sourceFunctions, ignoreDefault, source_functions_1.SourceFunctions);
+    const readFunctions = getFunctionsToCheck(query.readFunctions, ignoreDefault, read_functions_1.ReadFunctions);
+    const writeFunctions = getFunctionsToCheck(query.writeFunctions, ignoreDefault, write_functions_1.WriteFunctions);
     const numberOfFunctions = libraryFunctions.length + sourceFunctions.length + readFunctions.length + writeFunctions.length;
     const results = numberOfFunctions === 0 ? { kinds: {}, '.meta': { timing: 0 } } : (0, query_1.executeQueriesOfSameType)(data, ...makeCallContextQuery(libraryFunctions, 'library'), ...makeCallContextQuery(sourceFunctions, 'source'), ...makeCallContextQuery(readFunctions, 'read'), ...makeCallContextQuery(writeFunctions, 'write'));
     function getLexeme(argument, id) {
@@ -113,6 +118,9 @@ function getResults(data, results, kind, functions, makeInfo) {
         const linkedArgs = collectValuesFromLinks(args, data, linkedIds);
         const foundValues = linkedArgs ?? args;
         if (!foundValues) {
+            if (info.ignoreIf === 'arg-missing') {
+                return [];
+            }
             const record = (0, objects_1.compactRecord)(makeInfo(id, vertex, undefined, undefined, dropInfoOnLinkedIds(linkedIds)));
             return record ? [record] : [];
         }
@@ -140,7 +148,7 @@ function collectValuesFromLinks(args, data, linkedIds) {
         }
         const info = linkedId.info;
         // do not collect this one
-        if (hasAtLeastAValue && info.when !== dependencies_query_format_1.DependencyInfoLinkConstraint.Always) {
+        if (hasAtLeastAValue && info.when !== function_info_1.DependencyInfoLinkConstraint.Always) {
             continue;
         }
         // collect this one!

package/queries/catalog/dependencies-query/dependencies-query-format.d.ts

@@ -2,32 +2,8 @@ import type { BaseQueryFormat, BaseQueryResult } from '../../base-query-format';
 import type { NodeId } from '../../../r-bridge/lang-4.x/ast/model/processing/node-id';
 import Joi from 'joi';
 import { executeDependenciesQuery } from './dependencies-query-executor';
-import type { LinkTo } from '../call-context-query/call-context-query-format';
+import type { FunctionInfo } from './function-info/function-info';
 export declare const Unknown = "unknown";
-/** when to read the argument value from a linked function */
-export declare enum DependencyInfoLinkConstraint {
-    Always = "always",
-    IfUnknown = "if-unknown"
-}
-/**
- * A dependency link may have attached information. If you pass it, we try to resolve the argument value from the linked function
- * if the `when` constraint is met.
- */
-export type DependencyInfoLink = LinkTo<RegExp | string, Omit<FunctionInfo, 'name' | 'linkTo'> & {
-    when: DependencyInfoLinkConstraint;
-} | undefined>;
-export type DependencyInfoLinkAttachedInfo = DependencyInfoLink['attachLinkInfo'];
-export declare const LibraryFunctions: FunctionInfo[];
-export declare const SourceFunctions: FunctionInfo[];
-export declare const ReadFunctions: FunctionInfo[];
-export declare const WriteFunctions: FunctionInfo[];
-export interface FunctionInfo {
-    name: string;
-    argIdx?: number | 'unnamed';
-    argName?: string;
-    linkTo?: DependencyInfoLink[];
-    resolveValue?: boolean | 'library';
-}
 export interface DependenciesQuery extends BaseQueryFormat {
     readonly type: 'dependencies';
     readonly ignoreDefaultFunctions?: boolean;

package/queries/catalog/dependencies-query/dependencies-query-format.js

@@ -3,156 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DependenciesQueryDefinition = exports.WriteFunctions = exports.ReadFunctions = exports.SourceFunctions = exports.LibraryFunctions = exports.DependencyInfoLinkConstraint = exports.Unknown = void 0;
+exports.DependenciesQueryDefinition = exports.Unknown = void 0;
 const ansi_1 = require("../../../util/ansi");
 const time_1 = require("../../../util/time");
 const joi_1 = __importDefault(require("joi"));
 const dependencies_query_executor_1 = require("./dependencies-query-executor");
 exports.Unknown = 'unknown';
-/** when to read the argument value from a linked function */
-var DependencyInfoLinkConstraint;
-(function (DependencyInfoLinkConstraint) {
-    DependencyInfoLinkConstraint["Always"] = "always";
-    DependencyInfoLinkConstraint["IfUnknown"] = "if-unknown";
-})(DependencyInfoLinkConstraint || (exports.DependencyInfoLinkConstraint = DependencyInfoLinkConstraint = {}));
-// these lists are originally based on https://github.com/duncantl/CodeDepends/blob/7fd96dfee16b252e5f642c77a7ababf48e9326f8/R/codeTypes.R
-exports.LibraryFunctions = [
-    { name: 'library', argIdx: 0, argName: 'package', resolveValue: 'library' },
-    { name: 'require', argIdx: 0, argName: 'package', resolveValue: 'library' },
-    { name: 'loadNamespace', argIdx: 0, argName: 'package', resolveValue: true },
-    { name: 'attachNamespace', argIdx: 0, argName: 'ns', resolveValue: true },
-    { name: 'attach', argIdx: 0, argName: 'what', resolveValue: true },
-    { name: 'groundhog.library', argIdx: 0, argName: 'pkg', resolveValue: true },
-    { name: 'p_load', argIdx: 'unnamed', resolveValue: 'library' }, // pacman
-    { name: 'p_load_gh', argIdx: 'unnamed', resolveValue: 'library' }, // pacman
-    { name: 'from_import', argIdx: 0, argName: 'package', resolveValue: true }, // easypackages
-    { name: 'libraries', argIdx: 'unnamed', resolveValue: true }, // easypackages
-    { name: 'shelf', argIdx: 'unnamed', resolveValue: true } // librarian
-];
-exports.SourceFunctions = [
-    { name: 'source', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'sys.source', argIdx: 0, argName: 'file', resolveValue: true }
-];
-exports.ReadFunctions = [
-    { name: 'read.table', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.csv', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.csv2', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.delim', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.dcf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'scan', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.fwf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'file', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'url', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'load', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'gzfile', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'bzfile', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'download.file', argIdx: 0, argName: 'url', resolveValue: true },
-    { name: 'pipe', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'fifo', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'unz', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'matrix', argIdx: 0, argName: 'data', resolveValue: true },
-    { name: 'readRDS', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'readLines', argIdx: 0, argName: 'con', resolveValue: true },
-    { name: 'readRenviron', argIdx: 0, argName: 'path', resolveValue: true },
-    // readr
-    { name: 'read_csv', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_csv2', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_lines', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_delim', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_dsv', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_fwf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_tsv', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_table', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_log', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_lines', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_lines_chunked', argIdx: 0, argName: 'file', resolveValue: true },
-    // xlsx
-    { name: 'read.xlsx', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.xlsx2', argIdx: 0, argName: 'file', resolveValue: true },
-    // data.table
-    { name: 'fread', argIdx: 0, argName: 'file', resolveValue: true },
-    // haven
-    { name: 'read_sas', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_sav', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_por', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_dta', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_xpt', argIdx: 0, argName: 'file', resolveValue: true },
-    // feather
-    { name: 'read_feather', argIdx: 0, argName: 'file', resolveValue: true },
-    // foreign
-    { name: 'read.arff', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.dbf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.dta', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.epiinfo', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.mtp', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.octave', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.spss', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.ssd', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.systat', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.xport', argIdx: 0, argName: 'file', resolveValue: true },
-    // car
-    { name: 'Import', argIdx: 0, argName: 'file', resolveValue: true },
-];
-const OutputRedirects = [
-    { type: 'link-to-last-call', callName: 'sink', attachLinkInfo: { argIdx: 0, argName: 'file', when: DependencyInfoLinkConstraint.IfUnknown, resolveValue: true } }
-];
-exports.WriteFunctions = [
-    { name: 'save', argName: 'file', resolveValue: true },
-    { name: 'save.image', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'dput', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'dump', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.table', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.csv', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'saveRDS', argIdx: 1, argName: 'file', resolveValue: true },
-    // write functions that don't have argIndex are assumed to write to stdout
-    { name: 'print', linkTo: OutputRedirects, resolveValue: true },
-    { name: 'cat', linkTo: OutputRedirects, argName: 'file', resolveValue: true },
-    { name: 'message', linkTo: OutputRedirects, resolveValue: true },
-    { name: 'warning', linkTo: OutputRedirects, resolveValue: true },
-    // readr
-    { name: 'write_csv', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_csv2', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_delim', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_dsv', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_fwf', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_tsv', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_table', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_log', argIdx: 1, argName: 'file', resolveValue: true },
-    // heaven
-    { name: 'write_sas', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_sav', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_por', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_dta', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_xpt', argIdx: 1, argName: 'file', resolveValue: true },
-    // feather
-    { name: 'write_feather', argIdx: 1, argName: 'file', resolveValue: true },
-    // foreign
-    { name: 'write.arff', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.dbf', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.dta', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.foreign', argIdx: 1, argName: 'file', resolveValue: true },
-    // xlsx
-    { name: 'write.xlsx', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.xlsx2', argIdx: 1, argName: 'file', resolveValue: true },
-    // graphics
-    { name: 'pdf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'jpeg', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'png', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'windows', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'postscript', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'xfix', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'bitmap', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'pictex', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'cairo_pdf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'svg', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'bmp', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'tiff', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'X11', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'quartz', argIdx: 0, argName: 'file', resolveValue: true },
-    // car
-    { name: 'Export', argIdx: 0, argName: 'file', resolveValue: true },
-];
 function printResultSection(title, infos, result, sectionSpecifics) {
     if (infos.length <= 0) {
         return;
@@ -175,6 +31,7 @@ function printResultSection(title, infos, result, sectionSpecifics) {
 }
 const functionInfoSchema = joi_1.default.array().items(joi_1.default.object({
     name: joi_1.default.string().required().description('The name of the library function.'),
+    package: joi_1.default.string().optional().description('The package name of the library function'),
     argIdx: joi_1.default.number().optional().description('The index of the argument that contains the library name.'),
     argName: joi_1.default.string().optional().description('The name of the argument that contains the library name.'),
 })).optional();

package/queries/catalog/dependencies-query/function-info/function-info.d.ts

@@ -0,0 +1,24 @@
+import type { LinkTo } from '../../call-context-query/call-context-query-format';
+/** when to read the argument value from a linked function */
+export declare enum DependencyInfoLinkConstraint {
+    Always = "always",
+    IfUnknown = "if-unknown"
+}
+/**
+ * A dependency link may have attached information. If you pass it, we try to resolve the argument value from the linked function
+ * if the `when` constraint is met.
+ */
+export type DependencyInfoLink = LinkTo<RegExp | string, Omit<FunctionInfo, 'name' | 'linkTo' | 'package'> & {
+    when: DependencyInfoLinkConstraint;
+} | undefined>;
+export type DependencyInfoLinkAttachedInfo = DependencyInfoLink['attachLinkInfo'];
+export interface FunctionInfo {
+    package?: string;
+    name: string;
+    /** the index if the argument can be positional, unnamed in case of something like `...`, if the argument must be given with the name, please leave undefined */
+    argIdx?: number | 'unnamed';
+    argName?: string;
+    linkTo?: DependencyInfoLink[];
+    resolveValue?: boolean | 'library';
+    ignoreIf?: 'arg-missing';
+}

package/queries/catalog/dependencies-query/function-info/function-info.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DependencyInfoLinkConstraint = void 0;
+/** when to read the argument value from a linked function */
+var DependencyInfoLinkConstraint;
+(function (DependencyInfoLinkConstraint) {
+    DependencyInfoLinkConstraint["Always"] = "always";
+    DependencyInfoLinkConstraint["IfUnknown"] = "if-unknown";
+})(DependencyInfoLinkConstraint || (exports.DependencyInfoLinkConstraint = DependencyInfoLinkConstraint = {}));
+//# sourceMappingURL=function-info.js.map

package/queries/catalog/dependencies-query/function-info/library-functions.d.ts

@@ -0,0 +1,2 @@
+import type { FunctionInfo } from './function-info';
+export declare const LibraryFunctions: FunctionInfo[];

package/queries/catalog/dependencies-query/function-info/library-functions.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LibraryFunctions = void 0;
+exports.LibraryFunctions = [
+    { package: 'base', name: 'library', argIdx: 0, argName: 'package', resolveValue: 'library' },
+    { package: 'base', name: 'require', argIdx: 0, argName: 'package', resolveValue: 'library' },
+    { package: 'base', name: 'loadNamespace', argIdx: 0, argName: 'package', resolveValue: true },
+    { package: 'base', name: 'attachNamespace', argIdx: 0, argName: 'ns', resolveValue: true },
+    { package: 'base', name: 'attach', argIdx: 0, argName: 'what', resolveValue: true },
+    { package: 'groundhog', name: 'groundhog.library', argIdx: 0, argName: 'pkg', resolveValue: true },
+    { package: 'pacman', name: 'p_load', argIdx: 'unnamed', resolveValue: 'library' },
+    { package: 'pacman', name: 'p_load_gh', argIdx: 'unnamed', resolveValue: 'library' },
+    { package: 'easypackages', name: 'from_import', argIdx: 0, argName: 'package', resolveValue: true },
+    { package: 'easypackages', name: 'libraries', argIdx: 'unnamed', resolveValue: true },
+    { package: 'librarian', name: 'shelf', argIdx: 'unnamed', resolveValue: true },
+    { package: 'devtools', name: 'load_all', argIdx: 0, argName: 'path', resolveValue: true }
+];
+//# sourceMappingURL=library-functions.js.map

package/queries/catalog/dependencies-query/function-info/read-functions.d.ts

@@ -0,0 +1,2 @@
+import type { FunctionInfo } from './function-info';
+export declare const ReadFunctions: FunctionInfo[];

package/queries/catalog/dependencies-query/function-info/read-functions.js

@@ -0,0 +1,101 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ReadFunctions = void 0;
+exports.ReadFunctions = [
+    { package: 'base', name: 'parse', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'base', name: 'read.table', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'read.csv', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'read.csv2', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'read.delim', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'read.dcf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'scan', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'read.fwf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'file', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'url', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'load', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'gzfile', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'bzfile', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'utils', name: 'download.file', argIdx: 0, argName: 'url', resolveValue: true },
+    { package: 'base', name: 'pipe', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'fifo', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'unz', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'matrix', argIdx: 0, argName: 'data', resolveValue: true },
+    { package: 'base', name: 'readRDS', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'readLines', argIdx: 0, argName: 'con', resolveValue: true },
+    { package: 'base', name: 'readRenviron', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'readr', name: 'read_csv', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_csv2', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_lines', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_delim', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_dsv', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_fwf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_tsv', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_table', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_log', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_lines_raw', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_lines_chunked', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_rds', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'clipboard' },
+    { package: 'xlsx', name: 'read.xlsx', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'xlsx', name: 'read.xlsx2', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'data.table', name: 'fread', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_sas', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_sav', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_por', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_dta', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_xpt', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'feather', name: 'read_feather', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.arff', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.dbf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.dta', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.epiinfo', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.mtp', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.octave', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.spss', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.ssd', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.systat', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.xport', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'car', name: 'Import', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'magick', name: 'image_read', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'magick', name: 'image_read_svg', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'magick', name: 'image_read_pdf', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'magick', name: 'image_read_video', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'LIM', name: 'Read', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'sourcetools', name: 'read', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sourcetools', name: 'read_lines', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sourcetools', name: 'read_bytes', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sourcetools', name: 'read_lines_bytes', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sourcetools', name: 'tokenize', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'sourcetools', name: 'tokenize_file', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'expss', name: 'read_spss', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'expss', name: 'read_spss_to_list', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'SimPhe', name: 'read.geno', argIdx: 0, argName: 'fname', resolveValue: true },
+    { package: 'ape', name: 'read.tree', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'geomorph', name: 'readland.tps', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readxl', name: 'read_excel', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'readxl', name: 'read_xls', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'readxl', name: 'read_xlsx', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sf', name: 'read.sf', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'sf', name: 'st_read', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'readOGR', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'ogrInfo', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'ogrFIDs', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'OGRSpatialRef', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'ogrListLayers', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'readGDAL', argIdx: 0, argName: 'fname', resolveValue: true },
+    { package: 'readstata13', name: 'read.dta13', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'arrow', name: 'read_parquet', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'maptools', name: 'readShapePoly', argIdx: 0, argName: 'fn', resolveValue: true },
+    { package: 'XLConnect', name: 'readWorksheetFromFile', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'XLConnect', name: 'readNamedRegionFromFile', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'XLConnect', name: 'loadWorkbook', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'DiagrammeR', name: 'import_graph', argIdx: 0, argName: 'graph_file', resolveValue: true },
+    { package: 'DiagrammeR', name: 'open_graph', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'highcharter', name: 'download_map_data', argIdx: 0, argName: 'url', resolveValue: true },
+    { package: 'rvest', name: 'read_html', argIdx: 0, argName: 'x', resolveValue: true },
+    { package: 'rvest', name: 'read_html_live', argIdx: 0, argName: 'url', resolveValue: true },
+    { package: 'stats', name: 'read.ftable', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'DBI', name: 'dbReadTable', argIdx: 1, argName: 'name', resolveValue: true },
+    { package: 'DBI', name: 'dbReadTableArrow', argIdx: 1, argName: 'name', resolveValue: true },
+];
+//# sourceMappingURL=read-functions.js.map

package/queries/catalog/dependencies-query/function-info/source-functions.d.ts

@@ -0,0 +1,2 @@
+import type { FunctionInfo } from './function-info';
+export declare const SourceFunctions: FunctionInfo[];

package/queries/catalog/dependencies-query/function-info/source-functions.js

@@ -0,0 +1,11 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SourceFunctions = void 0;
+// these lists are originally based on https://github.com/duncantl/CodeDepends/blob/7fd96dfee16b252e5f642c77a7ababf48e9326f8/R/codeTypes.R
+exports.SourceFunctions = [
+    { package: 'base', name: 'source', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'sys.source', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'devtools', name: 'source_url', argIdx: 0, argName: 'url', resolveValue: true },
+    { package: 'devtools', name: 'source_gist', argIdx: 0, argName: 'id', resolveValue: true }
+];
+//# sourceMappingURL=source-functions.js.map

package/queries/catalog/dependencies-query/function-info/write-functions.d.ts

@@ -0,0 +1,2 @@
+import { type FunctionInfo } from './function-info';
+export declare const WriteFunctions: FunctionInfo[];

package/queries/catalog/dependencies-query/function-info/write-functions.js

@@ -0,0 +1,87 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.WriteFunctions = void 0;
+const function_info_1 = require("./function-info");
+const OutputRedirects = [
+    { type: 'link-to-last-call', callName: 'sink', attachLinkInfo: { argIdx: 0, argName: 'file', when: function_info_1.DependencyInfoLinkConstraint.IfUnknown, resolveValue: true } }
+];
+exports.WriteFunctions = [
+    { package: 'base', name: 'save', argName: 'file', resolveValue: true },
+    { package: 'base', name: 'save.image', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'write', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'dput', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'dump', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'write.table', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'write.csv', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'saveRDS', argIdx: 1, argName: 'file', resolveValue: true },
+    // write functions that don't have argIndex are assumed to write to stdout
+    { package: 'base', name: 'print', linkTo: OutputRedirects, resolveValue: true },
+    { package: 'base', name: 'cat', linkTo: OutputRedirects, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'message', linkTo: OutputRedirects, resolveValue: true },
+    { package: 'base', name: 'warning', linkTo: OutputRedirects, resolveValue: true },
+    { package: 'readr', name: 'write_csv', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_csv2', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_delim', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_dsv', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_fwf', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_tsv', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_table', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_log', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_lines', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_rds', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_sas', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_sav', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_por', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_dta', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_xpt', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'feather', name: 'write_feather', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'write.arff', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'write.dbf', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'write.dta', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'write.foreign', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'xlsx', name: 'write.xlsx', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'xlsx', name: 'write.xlsx2', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'pdf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'jpeg', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'png', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'windows', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'postscript', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'xfix', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'bitmap', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'pictex', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'cairo_pdf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'svg', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'bmp', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'tiff', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'X11', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'quartz', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'car', name: 'Export', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'LIM', name: 'PrintMat', linkTo: OutputRedirects, resolveValue: true },
+    { package: 'sjmisc', name: 'write_spss', argIdx: 1, argName: 'path', resolveValue: true },
+    { package: 'sjmisc', name: 'write_stata', argIdx: 1, argName: 'path', resolveValue: true },
+    { package: 'sjmisc', name: 'write_sas', argIdx: 1, argName: 'path', resolveValue: true },
+    { package: 'ape', name: 'write.tree', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'ape', name: 'write.nexus', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'ape', name: 'write.phyloXML', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'Claddis', name: 'write_nexus_matrix', argIdx: 1, argName: 'file_name', resolveValue: true },
+    { package: 'Claddis', name: 'write_tnt_matrix', argIdx: 1, argName: 'file_name', resolveValue: true },
+    { package: 'rgdal', name: 'writeOGR', argIdx: 1, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'writeGDAL', argIdx: 1, argName: 'fname', resolveValue: true },
+    { package: 'arrow', name: 'write_parquet', argIdx: 1, argName: 'sink', resolveValue: true },
+    { package: 'sf', name: 'st_write', argIdx: 1, argName: 'dsn', resolveValue: true },
+    { package: 'sf', name: 'write_sf', argIdx: 1, argName: 'dsn', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'maptools', name: 'writePolyShape', argIdx: 1, argName: 'fn', resolveValue: true },
+    { package: 'XLConnect', name: 'writeNamedRegionToFile', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'XLConnect', name: 'writeWorksheetToFile', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'visNetwork', name: 'visSave', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'DiagrammeR', name: 'save_graph', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'DiagrammeR', name: 'export_graph', argName: 'file_name', resolveValue: true },
+    { package: 'ggplot', name: 'ggsave', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'cowplot', name: 'ggsave2', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'tinyplot', name: 'tinyplot', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'tinyplot', name: 'plt', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rasterpdf', name: 'raster_pdf', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'rasterpdf', name: 'agg_pdf', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'highcharter', name: 'hc_exporting', argName: 'filename', resolveValue: true },
+];
+//# sourceMappingURL=write-functions.js.map

package/queries/catalog/location-map-query/location-map-query-executor.d.ts

@@ -1,3 +1,3 @@
 import type { LocationMapQuery, LocationMapQueryResult } from './location-map-query-format';
 import type { BasicQueryData } from '../../base-query-format';
-export declare function executeLocationMapQuery({ ast }: BasicQueryData, queries: readonly LocationMapQuery[]): LocationMapQueryResult;
+export declare function executeLocationMapQuery({ ast, dataflow: { graph } }: BasicQueryData, queries: readonly LocationMapQuery[]): LocationMapQueryResult;

package/queries/catalog/location-map-query/location-map-query-executor.js

@@ -2,14 +2,49 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.executeLocationMapQuery = executeLocationMapQuery;
 const log_1 = require("../../../util/log");
-function executeLocationMapQuery({ ast }, queries) {
+const fileIdRegex = /^(?<file>.*(\.[rR]))-/;
+function fuzzyFindFile(node, idMap) {
+    if (node?.info.file) {
+        return node.info.file;
+    }
+    else if (node?.info.id) {
+        const file = fileIdRegex.exec(String(node.info.id));
+        if (file && file.groups?.file.trim()) {
+            return file.groups?.file.trim();
+        }
+    }
+    else if (node?.info.parent) {
+        const parent = idMap.get(node.info.parent);
+        if (parent) {
+            return fuzzyFindFile(parent, idMap);
+        }
+    }
+    return '<inline>';
+}
+function executeLocationMapQuery({ ast, dataflow: { graph } }, queries) {
     if (queries.length !== 1) {
         log_1.log.warn('Id-Map query expects only up to one query, but got', queries.length);
     }
     const start = Date.now();
-    const locationMap = {};
+    const locationMap = {
+        files: {},
+        ids: {}
+    };
+    let count = 0;
+    const inverseMap = new Map();
+    for (const file of graph.sourced) {
+        locationMap.files[count] = file;
+        inverseMap.set(file, count);
+        count++;
+    }
     for (const [id, node] of ast.idMap.entries()) {
-        locationMap[id] = node.location;
+        if (node.location) {
+            const file = fuzzyFindFile(node, ast.idMap);
+            locationMap.ids[id] = [
+                inverseMap.get(file) ?? -1,
+                node.location
+            ];
+        }
     }
     return {
         '.meta': {

package/queries/catalog/location-map-query/location-map-query-format.d.ts

@@ -7,8 +7,17 @@ import type { SourceRange } from '../../../util/range';
 export interface LocationMapQuery extends BaseQueryFormat {
     readonly type: 'location-map';
 }
+export type FileId = number & {
+    readonly __fileId?: unique symbol;
+};
+export type FilePath = string & {
+    readonly __filePath?: unique symbol;
+};
 export interface LocationMapQueryResult extends BaseQueryResult {
-    readonly map: Record<NodeId, SourceRange | undefined>;
+    readonly map: {
+        files: Record<FileId, FilePath>;
+        ids: Record<NodeId, [FileId, SourceRange]>;
+    };
 }
 export declare const LocationMapQueryDefinition: {
     readonly executor: typeof executeLocationMapQuery;