@eagleoutice/flowr 2.1.4 → 2.1.6

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

@@ -4,9 +4,11 @@ import { PipelineStepStage } from '../../pipeline-step';
 import type { IdGenerator } from '../../../../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { NoInfo } from '../../../../r-bridge/lang-4.x/ast/model/model';
 import type { ParseStepOutput } from './00-parse';
+import type { RParseRequests } from '../../../../r-bridge/retriever';
 export interface NormalizeRequiredInput {
     /** This id generator is only necessary if you want to retrieve a dataflow from the parsed R AST, it determines the id generator to use and by default uses the {@link deterministicCountingIdGenerator}*/
     readonly getId?: IdGenerator<NoInfo>;
+    readonly request: RParseRequests;
 }
 declare function processor(results: {
     parse?: ParseStepOutput;

package/core/steps/all/core/10-normalize.js

@@ -4,8 +4,19 @@ exports.NORMALIZE = void 0;
 const print_1 = require("../../../print/print");
 const normalize_printer_1 = require("../../../print/normalize-printer");
 const parser_1 = require("../../../../r-bridge/lang-4.x/ast/parser/json/parser");
+function getCurrentRequestFile(request) {
+    if (request === undefined) {
+        return undefined;
+    }
+    else if (Array.isArray(request)) {
+        return request[0].request === 'file' ? request[0].content : undefined;
+    }
+    else {
+        return request.request === 'file' ? request.content : undefined;
+    }
+}
 function processor(results, input) {
-    return (0, parser_1.normalize)(results.parse, input.getId);
+    return (0, parser_1.normalize)(results.parse, input.getId, getCurrentRequestFile(input.request));
 }
 exports.NORMALIZE = {
     name: 'normalize',

package/dataflow/environments/identifier.d.ts

@@ -6,7 +6,7 @@ export type Identifier = string & {
 };
 /**
  * Each reference only has exactly one reference type, stored as the respective number.
- * However, wenn checking we may want to allow for one of several types,
+ * However, when checking we may want to allow for one of several types,
  * allowing the combination of the respective bitmasks.
  */
 export declare enum ReferenceType {

package/dataflow/environments/identifier.js

@@ -4,7 +4,7 @@ exports.ReferenceTypeReverseMapping = exports.ReferenceType = void 0;
 exports.isReferenceType = isReferenceType;
 /**
  * Each reference only has exactly one reference type, stored as the respective number.
- * However, wenn checking we may want to allow for one of several types,
+ * However, when checking we may want to allow for one of several types,
  * allowing the combination of the respective bitmasks.
  */
 var ReferenceType;

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

@@ -67,7 +67,7 @@ function sourceRequest(rootId, request, data, information, getId) {
     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, request.request === 'file' ? request.content : undefined);
         dataflow = (0, processor_1.processDataflowFor)(normalized.ast, {
             ...data,
             currentRequest: request,
@@ -81,7 +81,9 @@ function sourceRequest(rootId, request, data, information, getId) {
         return information;
     }
     // take the entry point as well as all the written references, and give them a control dependency to the source call to show that they are conditional
-    dataflow.graph.addControlDependency(dataflow.entryPoint, rootId);
+    if (dataflow.graph.hasVertex(dataflow.entryPoint)) {
+        dataflow.graph.addControlDependency(dataflow.entryPoint, rootId);
+    }
     for (const out of dataflow.out) {
         dataflow.graph.addControlDependency(out.nodeId, rootId);
     }

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

@@ -1,6 +1,9 @@
 export declare const FlowrGithubBaseRef = "https://github.com/flowr-analysis";
+export declare const FlowrSiteBaseRef = "https://flowr-analysis.github.io/flowr";
 export declare const RemoteFlowrFilePathBaseRef = "https://github.com/flowr-analysis/flowr/tree/main/";
 export declare const FlowrWikiBaseRef = "https://github.com/flowr-analysis/flowr/wiki/";
 export declare const FlowrNpmRef = "https://www.npmjs.com/package/@eagleoutice/flowr";
+export declare const FlowrDockerRef = "https://hub.docker.com/r/eagleoutice/flowr";
+export declare const FlowrCodecovRef = "https://app.codecov.io/gh/flowr-analysis/flowr";
 export declare function getFilePathMd(path: string): string;
 export declare function getFileContentFromRoot(path: string): string;

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

@@ -3,18 +3,23 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.FlowrNpmRef = exports.FlowrWikiBaseRef = exports.RemoteFlowrFilePathBaseRef = exports.FlowrGithubBaseRef = void 0;
+exports.FlowrCodecovRef = exports.FlowrDockerRef = exports.FlowrNpmRef = exports.FlowrWikiBaseRef = exports.RemoteFlowrFilePathBaseRef = exports.FlowrSiteBaseRef = exports.FlowrGithubBaseRef = void 0;
 exports.getFilePathMd = getFilePathMd;
 exports.getFileContentFromRoot = getFileContentFromRoot;
 const fs_1 = __importDefault(require("fs"));
 exports.FlowrGithubBaseRef = 'https://github.com/flowr-analysis';
+exports.FlowrSiteBaseRef = 'https://flowr-analysis.github.io/flowr';
 exports.RemoteFlowrFilePathBaseRef = `${exports.FlowrGithubBaseRef}/flowr/tree/main/`;
 exports.FlowrWikiBaseRef = `${exports.FlowrGithubBaseRef}/flowr/wiki/`;
 exports.FlowrNpmRef = 'https://www.npmjs.com/package/@eagleoutice/flowr';
+exports.FlowrDockerRef = 'https://hub.docker.com/r/eagleoutice/flowr';
+exports.FlowrCodecovRef = 'https://app.codecov.io/gh/flowr-analysis/flowr';
 function getFilePathMd(path) {
     // we go one up as we are in doc-util now :D #convenience
     const fullpath = require.resolve('../' + path);
-    const relative = fullpath.replace(process.cwd(), '.');
+    // normalize path separators so that this is consistent when testing on windows
+    const cwd = process.cwd().replaceAll('\\', '/');
+    const relative = fullpath.replaceAll('\\', '/').replace(cwd, '.');
     /* remove project prefix */
     return `[\`${relative}\`](${exports.RemoteFlowrFilePathBaseRef}${relative})`;
 }

package/documentation/print-linting-and-testing-wiki.d.ts

@@ -0,0 +1 @@
+export {};

package/documentation/print-linting-and-testing-wiki.js

@@ -0,0 +1,195 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const log_1 = require("../../test/functionality/_helper/log");
+const doc_code_1 = require("./doc-util/doc-code");
+const doc_files_1 = require("./doc-util/doc-files");
+function getText() {
+    return `
+For the latest code-coverage information, see [codecov.io](${doc_files_1.FlowrCodecovRef}), 
+for the latest benchmark results, see the [benchmark results](${doc_files_1.FlowrSiteBaseRef}/wiki/stats/benchmark) wiki page.
+
+- [Testing Suites](#testing-suites)
+  - [Functionality Tests](#functionality-tests)
+    - [Test Structure](#test-structure)
+    - [Writing a Test](#writing-a-test)
+    - [Running Only Some Tests](#running-only-some-tests)
+  - [Performance Tests](#performance-tests)
+  - [Oh no, the tests are slow](#oh-no-the-tests-are-slow)
+  - [Testing Within Your IDE](#testing-within-your-ide)
+    - [Using Visual Studio Code](#vs-code)
+    - [Using WebStorm](#webstorm)
+- [CI Pipeline](#ci-pipeline)
+- [Linting](#linting)
+  - [Oh no, the linter fails](#oh-no-the-linter-fails)
+  - [License Checker](#license-checker)
+
+## Testing Suites
+
+Currently, flowR contains two testing suites: one for [functionality](#functionality-tests) and one for [performance](#performance-tests). We explain each of them in the following.
+In addition to running those tests, you can use the more generalized \`npm run checkup\`. This will include the construction of the docker image, the generation of the wiki pages, and the linter.
+
+### Functionality Tests
+
+The functionality tests represent conventional unit (and depending on your terminology component/api) tests.
+We use [vitest](https://vitest.dev/) as our testing framework.
+You can run the tests by issuing:
+
+${(0, doc_code_1.codeBlock)('shell', 'npm run test')}
+
+Within the commandline,
+this should automatically drop you into a watch mode which will automatically re-run the tests if you change the code.
+If, at any time there are too many errors, you can use \`--bail=<value>\` to stop the tests after a certain number of errors.
+For example:
+
+${(0, doc_code_1.codeBlock)('shell', 'npm run test -- --bail=1')}
+
+If you want to run the tests without the watch mode, you can use:
+
+${(0, doc_code_1.codeBlock)('shell', 'npm run test -- --no-watch')}
+
+To run all tests, including a coverage report and label summary, run: 
+
+${(0, doc_code_1.codeBlock)('shell', 'npm run test-full')}
+
+However, depending on your local R version, your network connection and potentially other factors, some tests may be skipped automatically as they don't apply to your current system setup 
+(or can't be tested with the current prerequisites). 
+Each test can specify such requirements as part of the \`TestConfiguration\`, which is then used in the \`test.skipIf\` function of _vitest_.
+It is up to the [ci](#ci-pipeline) to run the tests on different systems to ensure that those tests are ensured to run.
+
+#### Test Structure
+
+All functionality tests are to be located under [test/functionality](${doc_files_1.RemoteFlowrFilePathBaseRef}test/functionality).
+
+This folder contains three special and important elements:
+
+- \`test-setup\` which is the entry point if *all* tests are run. It should automatically disable logging statements and configure global variables (e.g., if installation tests should run).
+- \`_helper\` which contains helper functions to be used by other tests.
+- \`test-summary\` which may produce a summary of the covered capabilities.
+
+We name all tests using the \`.test.ts\` suffix and try to run them in parallel. 
+Whenever this is not possible (e.g., when using \`withShell\`), please use \`describe.sequential\` to disable parallel execution for the respective test.
+
+#### Writing a Test
+
+Currently, this is heavily dependent on what you want to test (normalization, dataflow, quad-export, ...) 
+and it is probably best to have a look at existing tests in that area to get an idea of what comfort functionality is available.
+
+Generally, tests should be [labeled](${doc_files_1.RemoteFlowrFilePathBaseRef}test/functionality/_helper/label.ts) according to the *flowR* capabilities they test. The set of currently supported capabilities and their IDs can be found in ${(0, doc_files_1.getFilePathMd)('../r-bridge/data/data.ts')}. The resulting labels are used in the test report that is generated as part of the test output. They group tests by the capabilities they test and allow the report to display how many tests ensure that any given capability is properly supported. 
+
+Various helper functions are available to ease in writing tests with common behaviors, like testing for dataflow, slicing or query results. These can be found in [the \`_helper\` subdirectory](${doc_files_1.RemoteFlowrFilePathBaseRef}test/functionality/_helper).
+
+For example, an [existing test](${doc_files_1.RemoteFlowrFilePathBaseRef}test/functionality/dataflow/processing-of-elements/atomic/dataflow-atomic.test.ts) that tests the dataflow graph of a simple variable looks like this:
+${(0, doc_code_1.codeBlock)('typescript', `
+assertDataflow(label('simple variable', ['name-normal']), shell,
+	'x', emptyGraph().use('0', 'x')
+);
+`)}
+
+When writing dataflow tests, additional settings can be used to reduce the amount of graph data that needs to be pre-written. Notably:
+- \`expectIsSubgraph\` indicates that the expected graph is a subgraph, rather than the full graph that the test should generate. The test will then only check if the supplied graph is contained in the result graph, rather than an exact match.
+- \`resolveIdsAsCriterion\` indicates that the ids given in the expected (sub)graph should be resolved as [slicing criteria](${doc_files_1.FlowrWikiBaseRef}/Terminology#slicing-criterion) rather than actual ids. For example, passing \`12@a\` as an id in the expected (sub)graph will cause it to be resolved as the corresponding id.
+
+The following example shows both in use.
+${(0, doc_code_1.codeBlock)('typescript', `
+assertDataflow(label('without distractors', [...OperatorDatabase['<-'].capabilities, 'numbers', 'name-normal', 'newlines', 'name-escaped']),
+	shell, '\`a\` <- 2\\na',
+	emptyGraph()
+		.use('2@a')
+		.reads('2@a', '1@\`a\`'),
+	{
+		expectIsSubgraph:      true,
+		resolveIdsAsCriterion: true
+	}
+);
+`)}
+
+#### Running Only Some Tests
+
+To run only some tests, vitest allows you to [filter](https://vitest.dev/guide/filtering.html) tests. 
+Besides, you can use the watch mode (with \`npm run test\`) to only run tests that are affected by your changes.
+
+### Performance Tests
+
+The performance test suite of *flowR* uses several suites to check for variations in the required times for certain steps.
+Although we measure wall time in the CI (which is subject to rather large variations), it should give a rough idea of the performance of *flowR*.
+Furthermore, the respective scripts can be used locally as well.
+To run them, issue:
+
+${(0, doc_code_1.codeBlock)('shell', 'npm run performance-test')}
+
+See [test/performance](${doc_files_1.RemoteFlowrFilePathBaseRef}test/performance) for more information on the suites, how to run them, and their results. If you are interested in the results of the benchmarks, see [here](${doc_files_1.FlowrSiteBaseRef}/wiki/stats/benchmark).
+
+
+### Testing Within Your IDE
+
+#### VS Code
+
+Using the vitest Extension for Visual Studio Code, you can start tests directly from the definition and explore your suite in the Testing tab.
+To get started, install the [vitest Extension](https://marketplace.visualstudio.com/items?itemName=vitest.explorer).
+
+![vscode market place](img/vs-code-vitest.png)
+
+|               Testing Tab               | In Code                               |
+|:---------------------------------------:|:-------------------------------------:|
+| ![testing tab](img/testing-vs-code.png) | ![in code](img/testing-vs-code-2.png) |
+
+- Left-clicking the <img style="vertical-align: middle" src='img/circle-check-regular.svg' height='16pt'> or <img style="vertical-align: middle" src='img/circle-xmark-regular.svg' height='16pt'> Icon next to the code will rerun the test. Right-clicking will open a context menu, allowing you to debug the test.
+- In the Testing tab, you can run (and debug) all tests, individual suites or individual tests.
+
+#### Webstorm
+
+Please follow the official guide [here](https://www.jetbrains.com/help/webstorm/vitest.html).
+
+
+## CI Pipeline
+
+We have several workflows defined in [.github/workflows](../.github/workflows/).
+We explain the most important workflows in the following:
+
+- [qa.yaml](../.github/workflows/qa.yaml) is the main workflow that will run different steps depending on several factors. It is responsible for:
+  - running the [functionality](#functionality-tests) and [performance tests](#performance-tests)
+    - uploading the results to the [benchmark page](${doc_files_1.FlowrSiteBaseRef}/wiki/stats/benchmark) for releases
+    - running the [functionality tests](#functionality-tests) on different operating systems (Windows, macOS, Linux) and with different versions of R
+    - reporting code coverage
+  - running the [linter](#linting) and reporting its results
+  - deploying the documentation to [GitHub Pages](${doc_files_1.FlowrSiteBaseRef}/doc/)
+- [release.yaml](../.github/workflows/release.yaml) is responsible for creating a new release, only to be run by repository owners. Furthermore, it adds the new docker image to [docker hub](${doc_files_1.FlowrDockerRef}).
+- [broken-links-and-wiki.yaml](../.github/workflows/broken-links-and-wiki.yaml) repeatedly tests that all links are not dead!
+
+## Linting
+
+There are two linting scripts.
+The main one:
+
+${(0, doc_code_1.codeBlock)('shell', 'npm run lint')}
+
+And a weaker version of the first (allowing for *todo* comments) which is run automatically in the [pre-push githook](../.githooks/pre-push) as explained in the [CONTRIBUTING.md](../.github/CONTRIBUTING.md):
+
+${(0, doc_code_1.codeBlock)('shell', 'npm run lint-local')}
+
+Besides checking coding style (as defined in the [package.json](../package.json)), the *full* linter runs the [license checker](#license-checker).
+
+In case you are unaware,
+eslint can automatically fix several linting problems[](https://eslint.org/docs/latest/use/command-line-interface#fix-problems).
+So you may be fine by just running:
+
+${(0, doc_code_1.codeBlock)('shell', 'npm run lint-local -- --fix')}
+
+### Oh no, the linter fails
+
+By now, the rules should be rather stable and so, if the linter fails,
+it is usually best if you (if necessary) read the respective description and fix the respective problem.
+Rules in this project cover general JavaScript issues [using regular ESLint](https://eslint.org/docs/latest/rules), TypeScript-specific issues [using typescript-eslint](https://typescript-eslint.io/rules/), and code formatting [with ESLint Stylistic](https://eslint.style/packages/default#rules).
+
+However, in case you think that the linter is wrong, please do not hesitate to open a [new issue](${doc_files_1.FlowrGithubBaseRef}/flowr/issues/new/choose).
+
+### License Checker
+
+*flowR* is licensed under the [GPLv3 License](${doc_files_1.FlowrGithubBaseRef}/flowr/blob/main/LICENSE) requiring us to only rely on [compatible licenses](https://www.gnu.org/licenses/license-list.en.html). For now, this list is hardcoded as part of the npm [\`license-compat\`](../package.json) script so it can very well be that a new dependency you add causes the checker to fail &mdash; *even though it is compatible*. In that case, please either open a [new issue](${doc_files_1.FlowrGithubBaseRef}/flowr/issues/new/choose) or directly add the license to the list (including a reference to why it is compatible).
+`;
+}
+if (require.main === module) {
+    (0, log_1.setMinLevelOfAllLogs)(6 /* LogLevel.Fatal */);
+    console.log(getText());
+}
+//# sourceMappingURL=print-linting-and-testing-wiki.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.1.4",
+  "version": "2.1.6",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {
@@ -28,16 +28,18 @@
     "wiki:df-graph": "ts-node src/documentation/print-dataflow-graph-wiki.ts",
     "wiki:normalized-ast": "ts-node src/documentation/print-normalized-ast-wiki.ts",
     "wiki:query-api": "ts-node src/documentation/print-query-wiki.ts",
+    "wiki:linting-and-testing": "ts-node src/documentation/print-linting-and-testing-wiki.ts",
     "wiki:interface": "ts-node src/documentation/print-interface-wiki.ts",
     "build": "tsc --project .",
-    "build:bundle-flowr": "npm run build && esbuild --bundle dist/src/cli/flowr.js --platform=node --bundle --minify --target=node18 --outfile=dist/src/cli/flowr.min.js",
+    "build:bundle-flowr": "npm run build && esbuild --bundle dist/src/cli/flowr.js --platform=node --bundle --minify --target=node22 --outfile=dist/src/cli/flowr.min.js",
     "lint-local": "npx eslint --version && npx eslint src/ test/ --rule \"no-warning-comments: off\"",
     "lint": "npm run license-compat -- --summary && npx eslint --version && npx eslint src/ test/",
     "license-compat": "license-checker --onlyAllow 'MIT;MIT OR X11;GPLv2;LGPL;GNUGPL;ISC;Apache-2.0;FreeBSD;BSD-2-Clause;clearbsd;ModifiedBSD;BSD-3-Clause;Python-2.0;Unlicense;WTFPL;BlueOak-1.0.0;CC-BY-4.0;CC-BY-3.0;CC0-1.0;0BSD'",
     "doc": "typedoc",
-    "test": "nyc --no-clean mocha",
+    "test": "vitest --config test/vitest.config.mts",
+    "test:coverage": "npm run test -- --coverage",
     "performance-test": "func() { cd test/performance/ && bash run-all-suites.sh $1 $2 $3; cd ../../; }; func",
-    "test-full": "npm run test -- --test-installation",
+    "test-full": "npm run test:coverage -- --no-watch -- --make-summary --test-installation",
     "detect-circular-deps": "npx madge  --extensions ts,tsx --circular src/",
     "checkup": "npm run flowr -- --execute \":version\" && npm run lint && npm run test-full -- --forbid-only && docker build -t test-flowr -f scripts/Dockerfile . && npm run doc && npm-run-all wiki:*"
   },
@@ -51,33 +53,6 @@
   ],
   "author": "Florian Sihler",
   "license": "ISC",
-  "mocha": {
-    "require": "ts-node/register",
-    "timeout": 60000,
-    "spec": "test/**/*.spec.ts",
-    "source-map": true,
-    "recursive": true,
-    "exit": true,
-    "produce-source-map": true
-  },
-  "nyc": {
-    "all": true,
-    "per-file": true,
-    "check-coverage": false,
-    "skip-full": true,
-    "lines": 70,
-    "extension": [
-      ".ts"
-    ],
-    "include": [
-      "src/**/*.ts"
-    ],
-    "reporter": [
-      "text",
-      "lcov",
-      "cobertura"
-    ]
-  },
   "eslintConfig": {
     "settings": {
       "import/resolver": {
@@ -192,11 +167,8 @@
     "@commitlint/config-angular": "^19.3.0",
     "@eagleoutice/eslint-config-flowr": "^1.0.14",
     "@j-ulrich/release-it-regex-bumper": "^5.1.0",
-    "@types/chai": "^4.3.16",
-    "@types/chai-as-promised": "^7.1.8",
     "@types/command-line-args": "^5.2.3",
     "@types/command-line-usage": "^5.0.4",
-    "@types/mocha": "^10.0.6",
     "@types/n-readlines": "^1.0.6",
     "@types/n3": "^1.16.4",
     "@types/object-hash": "^3.0.6",
@@ -204,21 +176,19 @@
     "@types/tmp": "^0.2.6",
     "@types/ws": "^8.5.10",
     "@typescript-eslint/eslint-plugin": "^7.8.0",
-    "chai": "^4.3.16",
-    "chai-as-promised": "^7.1.1",
+    "@vitest/coverage-v8": "^2.1.4",
     "esbuild": "^0.23.1",
     "eslint": "^8.57.1",
     "license-checker": "^25.0.1",
-    "mocha": "^10.7.3",
-    "mocha-multi-reporters": "^1.5.1",
-    "nyc": "^17.0.0",
+    "npm-run-all": "^4.1.5",
     "release-it": "^17.6.0",
     "ts-node": "^10.9.2",
     "typedoc": "^0.26.7",
     "typedoc-plugin-missing-exports": "^3.0.0",
     "typedoc-theme-hierarchy": "^5.0.3",
     "typedoc-umlclass": "^0.10.0",
-    "typescript": "^5.6.2"
+    "typescript": "^5.6.2",
+    "vitest": "^2.1.4"
   },
   "dependencies": {
     "@xmldom/xmldom": "^0.9.2",

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

@@ -74,7 +74,7 @@ function makeCallContextQuery(functions, kind) {
     return functions.map(f => ({
         type: 'call-context',
         callName: f.name,
-        includeAliases: true,
+        includeAliases: false,
         callNameExact: true,
         subkind: f.name,
         linkTo: f.linkTo ? { type: 'link-to-last-call', callName: f.linkTo } : undefined,

package/r-bridge/lang-4.x/ast/model/model.d.ts

@@ -48,6 +48,10 @@ interface Source {
      * This allows inline-comments!
      */
     additionalTokens?: OtherInfoNode[];
+    /**
+     * The file in which the respective node is located
+     */
+    file?: string;
 }
 /**
  * Provides the common base of all {@link RNode|RNodes}.

package/r-bridge/lang-4.x/ast/model/processing/decorate.d.ts

@@ -75,14 +75,21 @@ export interface NormalizedAst<OtherInfo = ParentInformation, Node = RNode<Other
     /** The root of the AST with parent information */
     ast: Node;
 }
+export interface NormalizedAstDecorationConfiguration<OtherInfo> {
+    /** The id generator: must generate a unique id für each passed node */
+    getId?: IdGenerator<OtherInfo>;
+    /** the path to the file this AST was extracted from will be added to the nodes */
+    file?: string;
+}
 /**
  * Covert the given AST into a doubly linked tree while assigning ids (so it stays serializable).
  *
  * @param ast   - The root of the AST to convert
  * @param getId - The id generator: must generate a unique id für each passed node
+ * @param file  - the path to the file this AST was extracted from will be added to the nodes
  *
  * @typeParam OtherInfo - The original decoration of the ast nodes (probably is nothing as the id decoration is most likely the first step to be performed after extraction)
  *
  * @returns A decorated AST based on the input and the id provider.
  */
-export declare function decorateAst<OtherInfo = NoInfo>(ast: RNode<OtherInfo>, getId?: IdGenerator<OtherInfo>): NormalizedAst<OtherInfo & ParentInformation>;
+export declare function decorateAst<OtherInfo = NoInfo>(ast: RNode<OtherInfo>, { getId, file }: NormalizedAstDecorationConfiguration<OtherInfo>): NormalizedAst<OtherInfo & ParentInformation>;

package/r-bridge/lang-4.x/ast/model/processing/decorate.js

@@ -69,14 +69,15 @@ const nestForElement = new Set([
  *
  * @param ast   - The root of the AST to convert
  * @param getId - The id generator: must generate a unique id für each passed node
+ * @param file  - the path to the file this AST was extracted from will be added to the nodes
  *
  * @typeParam OtherInfo - The original decoration of the ast nodes (probably is nothing as the id decoration is most likely the first step to be performed after extraction)
  *
  * @returns A decorated AST based on the input and the id provider.
  */
-function decorateAst(ast, getId = deterministicCountingIdGenerator(0)) {
+function decorateAst(ast, { getId = deterministicCountingIdGenerator(0), file }) {
     const idMap = new bimap_1.BiMap();
-    const info = { idMap, getId };
+    const info = { idMap, getId, file };
     /* Please note, that all fold processors do not re-create copies in higher-folding steps so that the idMap stays intact. */
     const foldLeaf = createFoldForLeaf(info);
     const foldBinaryOp = createFoldForBinaryOp(info);
@@ -139,6 +140,7 @@ function createFoldForLeaf(info) {
                 nesting
             }
         };
+        decorated.info.file = info.file;
         info.idMap.set(id, decorated);
         return decorated;
     };
@@ -161,6 +163,7 @@ function createFoldForBinaryOp(info) {
             lhsInfo.role = "binop-lhs" /* RoleInParent.BinaryOperationLhs */;
             rhsInfo.role = "binop-rhs" /* RoleInParent.BinaryOperationRhs */;
         }
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -172,6 +175,7 @@ function createFoldForUnaryOp(info) {
         const opInfo = operand.info;
         opInfo.parent = id;
         opInfo.role = "unary-operand" /* RoleInParent.UnaryOperand */;
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -195,6 +199,7 @@ function createFoldForAccess(info) {
                 }
             }
         }
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -214,6 +219,7 @@ function createFoldForForLoop(info) {
         bodyInfo.parent = id;
         bodyInfo.index = 2;
         bodyInfo.role = "for-body" /* RoleInParent.ForBody */;
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -225,6 +231,7 @@ function createFoldForRepeatLoop(info) {
         const bodyInfo = body.info;
         bodyInfo.parent = id;
         bodyInfo.role = "repeat-body" /* RoleInParent.RepeatBody */;
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -240,6 +247,7 @@ function createFoldForWhileLoop(info) {
         bodyInfo.parent = id;
         bodyInfo.index = 1;
         bodyInfo.role = "while-body" /* RoleInParent.WhileBody */;
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -261,6 +269,7 @@ function createFoldForIfThenElse(info) {
             otherwiseInfo.index = 2;
             otherwiseInfo.role = "if-otherwise" /* RoleInParent.IfOtherwise */;
         }
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -276,6 +285,7 @@ function createFoldForExprList(info) {
             childInfo.index = i++;
             childInfo.role = "expr-list-child" /* RoleInParent.ExpressionListChild */;
         }
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -303,6 +313,7 @@ function createFoldForFunctionCall(info) {
                 argInfo.role = "call-argument" /* RoleInParent.FunctionCallArgument */;
             }
         }
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -322,6 +333,7 @@ function createFoldForFunctionDefinition(info) {
         bodyInfo.parent = id;
         bodyInfo.index = idx;
         bodyInfo.role = "function-def-body" /* RoleInParent.FunctionDefinitionBody */;
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -339,6 +351,7 @@ function createFoldForFunctionParameter(info) {
             defaultInfo.index = 1;
             defaultInfo.role = "param-value" /* RoleInParent.ParameterDefaultValue */;
         }
+        decorated.info.file = info.file;
         return decorated;
     };
 }
@@ -360,6 +373,7 @@ function createFoldForFunctionArgument(info) {
             valueInfo.index = idx;
             valueInfo.role = "arg-value" /* RoleInParent.ArgumentValue */;
         }
+        decorated.info.file = info.file;
         return decorated;
     };
 }

package/r-bridge/lang-4.x/ast/parser/json/parser.d.ts

@@ -2,4 +2,7 @@ import type { IdGenerator, NormalizedAst } from '../../model/processing/decorate
 import type { NoInfo } from '../../model/model';
 import type { ParseStepOutput } from '../../../../../core/steps/all/core/00-parse';
 export declare const parseLog: import("tslog").Logger<import("tslog").ILogObj>;
-export declare function normalize({ parsed }: ParseStepOutput, getId?: IdGenerator<NoInfo>): NormalizedAst;
+/**
+ * Take the output as produced by the parse step and normalize the AST from the R parser.
+ */
+export declare function normalize({ parsed }: ParseStepOutput, getId?: IdGenerator<NoInfo>, file?: string): NormalizedAst;

package/r-bridge/lang-4.x/ast/parser/json/parser.js

@@ -7,9 +7,12 @@ const log_1 = require("../../../../../util/log");
 const decorate_1 = require("../../model/processing/decorate");
 const normalize_root_1 = require("../main/internal/structure/normalize-root");
 exports.parseLog = log_1.log.getSubLogger({ name: 'ast-parser' });
-function normalize({ parsed }, getId = (0, decorate_1.deterministicCountingIdGenerator)(0)) {
+/**
+ * Take the output as produced by the parse step and normalize the AST from the R parser.
+ */
+function normalize({ parsed }, getId = (0, decorate_1.deterministicCountingIdGenerator)(0), file) {
     const data = { currentRange: undefined, currentLexeme: undefined };
     const object = (0, format_1.convertPreparedParsedData)((0, format_1.prepareParsedData)(parsed));
-    return (0, decorate_1.decorateAst)((0, normalize_root_1.normalizeRootObjToAst)(data, object), getId);
+    return (0, decorate_1.decorateAst)((0, normalize_root_1.normalizeRootObjToAst)(data, object), { getId, file });
 }
 //# sourceMappingURL=parser.js.map

package/r-bridge/retriever.d.ts

@@ -35,7 +35,7 @@ export type RParseRequests = RParseRequest | ReadonlyArray<RParseRequest>;
 export declare function requestFromInput(input: `${typeof fileProtocol}${string}`): RParseRequestFromFile;
 export declare function requestFromInput(input: `${typeof fileProtocol}${string}`[]): RParseRequestFromFile[];
 export declare function requestFromInput(input: string): RParseRequestFromText;
-export declare function requestFromInput(input: readonly string[]): RParseRequests;
+export declare function requestFromInput(input: readonly string[] | string): RParseRequests;
 export declare function requestProviderFromFile(): RParseRequestProvider;
 export declare function requestProviderFromText(text: Readonly<{
     [path: string]: string;

package/r-bridge/retriever.js

@@ -20,6 +20,7 @@ const object_hash_1 = __importDefault(require("object-hash"));
 const parser_1 = require("./lang-4.x/ast/parser/json/parser");
 const init_1 = require("./init");
 const convert_values_1 = require("./lang-4.x/convert-values");
+const decorate_1 = require("./lang-4.x/ast/model/processing/decorate");
 const type_1 = require("./lang-4.x/ast/model/type");
 exports.fileProtocol = 'file://';
 /**
@@ -92,7 +93,7 @@ function retrieveParseDataFromRCode(request, shell) {
  */
 async function retrieveNormalizedAstFromRCode(request, shell) {
     const data = await retrieveParseDataFromRCode(request, shell);
-    return (0, parser_1.normalize)({ parsed: data });
+    return (0, parser_1.normalize)({ parsed: data }, (0, decorate_1.deterministicCountingIdGenerator)(0), request.request === 'file' ? request.content : undefined);
 }
 /**
  * If the string has (R-)quotes around it, they will be removed; otherwise the string is returned unchanged.

package/util/version.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.flowrVersion = flowrVersion;
 const semver_1 = require("semver");
 // this is automatically replaced with the current version by release-it
-const version = '2.1.4';
+const version = '2.1.6';
 function flowrVersion() {
     return new semver_1.SemVer(version);
 }