@eagleoutice/flowr 2.1.12 → 2.2.0

package/r-bridge/shell-executor.d.ts

@@ -1,10 +1,46 @@
 import type { RShellExecutionOptions } from './shell';
 import type { SemVer } from 'semver';
-export declare class RShellExecutor {
+import type { SyncParser } from './parser';
+import { type RParseRequest } from './retriever';
+/**
+ * This is a synchronous alternative to the {@link RShell}.
+ * Please be aware that using this is expensive.
+ * Every request effectively causes a new initialization of the R interpreter.
+ *
+ * With this class you can {@link RShellExecutor#run|run(command)} commands,
+ * that are potentially decorated with {@link RShellExecutor#addPrerequisites|prerequisites}.
+ * For compatibility,
+ * we provide {@link RShellExecutor#parse|parse(request)} and {@link RShellExecutor#rVersion|rVersion()}.
+ */
+export declare class RShellExecutor implements SyncParser<string> {
+    readonly name = "r-shell";
     readonly options: Readonly<RShellExecutionOptions>;
     private readonly prerequisites;
     constructor(options?: Partial<RShellExecutionOptions>);
+    /**
+     * Adds commands that should be executed for every {@link RShellExecutor#run|run}.
+     */
     addPrerequisites(commands: string | string[]): this;
+    /**
+     * @returns the version of the R interpreter available to this executor.
+     *
+     * @see {@link RShellExecutor#usedRVersion}
+     * @see {@link RShell#rVersion}
+     * @see {@link RShell#usedRVersion}
+     */
+    rVersion(): Promise<string | 'unknown' | 'none'>;
+    /**
+     * Instead of returning a promise, this method returns the version of the R interpreter available to this executor,
+     * in the SemVer format.
+     */
     usedRVersion(): SemVer | null;
+    /**
+     * Runs the given command in the R interpreter.
+     */
     run(command: string, returnErr?: boolean): string;
+    /**
+     * Parses the given request and returns the result.
+     */
+    parse(request: RParseRequest): string;
+    close(): void;
 }

package/r-bridge/shell-executor.js

@@ -11,23 +11,55 @@ const preload_1 = __importDefault(require("semver/preload"));
 const log_1 = require("../util/log");
 const init_1 = require("./init");
 const convert_values_1 = require("./lang-4.x/convert-values");
+const retriever_1 = require("./retriever");
 const executorLog = log_1.log.getSubLogger({ name: 'RShellExecutor' });
+/**
+ * This is a synchronous alternative to the {@link RShell}.
+ * Please be aware that using this is expensive.
+ * Every request effectively causes a new initialization of the R interpreter.
+ *
+ * With this class you can {@link RShellExecutor#run|run(command)} commands,
+ * that are potentially decorated with {@link RShellExecutor#addPrerequisites|prerequisites}.
+ * For compatibility,
+ * we provide {@link RShellExecutor#parse|parse(request)} and {@link RShellExecutor#rVersion|rVersion()}.
+ */
 class RShellExecutor {
+    name = 'r-shell';
     options;
     prerequisites;
     constructor(options) {
         this.options = (0, objects_1.deepMergeObject)((0, shell_1.getDefaultRShellOptions)(), options);
         this.prerequisites = [(0, init_1.initCommand)(this.options.eol)];
     }
+    /**
+     * Adds commands that should be executed for every {@link RShellExecutor#run|run}.
+     */
     addPrerequisites(commands) {
         this.prerequisites.push(...(typeof commands == 'string' ? [commands] : commands));
         return this;
     }
+    /**
+     * @returns the version of the R interpreter available to this executor.
+     *
+     * @see {@link RShellExecutor#usedRVersion}
+     * @see {@link RShell#rVersion}
+     * @see {@link RShell#usedRVersion}
+     */
+    rVersion() {
+        return Promise.resolve(this.usedRVersion()?.format() ?? 'unknown');
+    }
+    /**
+     * Instead of returning a promise, this method returns the version of the R interpreter available to this executor,
+     * in the SemVer format.
+     */
     usedRVersion() {
         const version = this.run(`cat(paste0(R.version$major,".",R.version$minor), ${(0, convert_values_1.ts2r)(this.options.eol)})`);
         (0, log_1.expensiveTrace)(executorLog, () => `raw version: ${JSON.stringify(version)}`);
         return preload_1.default.coerce(version);
     }
+    /**
+     * Runs the given command in the R interpreter.
+     */
     run(command, returnErr = false) {
         command += ';base::quit()';
         (0, log_1.expensiveTrace)(executorLog, () => `> ${JSON.stringify(command)}`);
@@ -40,6 +72,13 @@ class RShellExecutor {
         });
         return (returnErr ? returns.stderr : returns.stdout).trim();
     }
+    /**
+     * Parses the given request and returns the result.
+     */
+    parse(request) {
+        return (0, retriever_1.retrieveParseDataFromRCode)(request, this);
+    }
+    close() { }
 }
 exports.RShellExecutor = RShellExecutor;
 //# sourceMappingURL=shell-executor.js.map

package/r-bridge/shell.d.ts

@@ -1,6 +1,8 @@
 import { type MergeableRecord } from '../util/objects';
 import type { SemVer } from 'semver';
 import type { AsyncOrSync } from 'ts-essentials';
+import type { AsyncParser } from './parser';
+import type { RParseRequest } from './retriever';
 export type OutputStreamSelector = 'stdout' | 'stderr' | 'both';
 export interface CollectorTimeout extends MergeableRecord {
     /**
@@ -72,22 +74,26 @@ export declare function getDefaultRShellOptions(): RShellOptions;
  * You can configure it by {@link RShellOptions}.
  *
  * At the moment we are using a live R session (and not networking etc.) to communicate with R easily,
- * which allows us to install packages etc. However, this might and probably will change in the future (leaving this
- * as a legacy mode :D)
+ * which allows us to install packages etc. However, this might and probably will change in the future
+ * (leaving this as a legacy mode :D)
  */
-export declare class RShell {
+export declare class RShell implements AsyncParser<string> {
+    readonly name = "r-shell";
+    readonly async = true;
     readonly options: Readonly<RShellOptions>;
     private session;
     private readonly log;
     private versionCache;
     private tempDirs;
     constructor(options?: Partial<RShellOptions>);
+    parse(request: RParseRequest): Promise<string>;
     private revive;
     /**
-   * sends the given command directly to the current R session
-   * will not do anything to alter input markers!
-   */
+     * sends the given command directly to the current R session
+     * will not do anything to alter input markers!
+     */
     sendCommand(command: string): void;
+    rVersion(): Promise<string | 'unknown' | 'none'>;
     usedRVersion(): Promise<SemVer | null>;
     injectLibPaths(...paths: readonly string[]): void;
     tryToInjectHomeLibPath(): void;

package/r-bridge/shell.js

@@ -38,6 +38,7 @@ const fs_1 = __importDefault(require("fs"));
 const init_1 = require("./init");
 const config_1 = require("../config");
 const convert_values_1 = require("./lang-4.x/convert-values");
+const retriever_1 = require("./retriever");
 exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = {
     from: 'stdout',
     postamble: `🐧${'-'.repeat(5)}🐧`,
@@ -54,7 +55,7 @@ let DEFAULT_R_SHELL_OPTIONS = undefined;
 function getDefaultRShellOptions() {
     if (!DEFAULT_R_SHELL_OPTIONS) {
         DEFAULT_R_SHELL_OPTIONS = {
-            pathToRExecutable: (0, config_1.getConfig)().rPath ?? exports.DEFAULT_R_PATH,
+            pathToRExecutable: (0, config_1.getEngineConfig)('r-shell')?.rPath ?? exports.DEFAULT_R_PATH,
             // -s is a short form of --no-echo (and the old version --slave), but this one works in R 3 and 4
             // (see https://github.com/wch/r-source/commit/f1ff49e74593341c74c20de9517f31a22c8bcb04)
             commandLineOptions: ['--vanilla', '--quiet', '--no-save', '-s'],
@@ -74,10 +75,12 @@ function getDefaultRShellOptions() {
  * You can configure it by {@link RShellOptions}.
  *
  * At the moment we are using a live R session (and not networking etc.) to communicate with R easily,
- * which allows us to install packages etc. However, this might and probably will change in the future (leaving this
- * as a legacy mode :D)
+ * which allows us to install packages etc. However, this might and probably will change in the future
+ * (leaving this as a legacy mode :D)
  */
 class RShell {
+    name = 'r-shell';
+    async = true;
     options;
     session;
     log;
@@ -90,6 +93,9 @@ class RShell {
         this.session = new RShellSession(this.options, this.log);
         this.revive();
     }
+    parse(request) {
+        return (0, retriever_1.retrieveParseDataFromRCode)(request, this);
+    }
     revive() {
         if (this.options.revive === 0 /* RShellReviveOptions.Never */) {
             return;
@@ -104,15 +110,18 @@ class RShell {
         });
     }
     /**
-   * sends the given command directly to the current R session
-   * will not do anything to alter input markers!
-   */
+     * sends the given command directly to the current R session
+     * will not do anything to alter input markers!
+     */
     sendCommand(command) {
         if (this.log.settings.minLevel <= 1 /* LogLevel.Trace */) {
             this.log.trace(`> ${JSON.stringify(command)}`);
         }
         this._sendCommand(command);
     }
+    async rVersion() {
+        return (await this.usedRVersion())?.format() ?? 'unknown';
+    }
     async usedRVersion() {
         if (this.versionCache !== null) {
             return this.versionCache;

package/search/search-optimizer/search-optimizer.js

@@ -71,7 +71,7 @@ function dropAnyNameRegex(generator) {
     if (generator.name !== 'get' || !generator.args.filter.nameIsRegex) {
         return generator;
     }
-    if (generator.args.filter.name === '.') {
+    if (generator.args.filter.name === '.*') {
         return {
             ...generator,
             args: {

package/statistics/statistics.js

@@ -82,7 +82,7 @@ function processMetaOnSuccessful(meta, request) {
 const parser = new xmldom_1.DOMParser();
 async function extractSingle(result, shell, request, features, suffixFilePath) {
     const slicerOutput = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
-        request, shell
+        request, parser: shell
     }).allRemainingSteps();
     // retrieve parsed xml through (legacy) xmlparsedata
     const suffix = request.request === 'file' ? ', encoding="utf-8"' : '';

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 = '2.1.12';
+const version = '2.2.0';
 function flowrVersion() {
     return new semver_1.SemVer(version);
 }