Fix: Prevent Reconstruction of Stub Functions in the Output (#1178)

* refactor: refine side effect triggers

* feat-fix: parameter recovery if empty

* feat-fix: type for parameter reconstruct

* refactor: trim parse data to prepare

src/dataflow/environments/default-builtin-config.ts

@@ -83,7 +83,7 @@ export const DefaultBuiltinConfig: BuiltInDefinitions = [
 			/* downloader and installer functions (R, devtools, BiocManager) */
 			'library.dynam', 'install.packages','install', 'install_github', 'install_gitlab', 'install_bitbucket', 'install_url', 'install_git', 'install_svn', 'install_local', 'install_version', 'update_packages',
 			/* weird env attachments */
-			'attach', 'detach', 'unname', 'rm', 'remove'
+			'attach', 'unname'
 		],
 		processor:       'builtin:default',
 		config:          { hasUnknownSideEffects: true },

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

@@ -80,7 +80,7 @@ function updateSideEffectsForCalledFunctions(calledEnvs: {
 	for(const { functionCall, called } of calledEnvs) {
 		const callDependencies = nextGraph.getVertex(functionCall, true)?.controlDependencies;
 		for(const calledFn of called) {
-			guard(calledFn.tag === VertexType.FunctionDefinition, 'called function must call a function definition');
+			guard(calledFn.tag === VertexType.FunctionDefinition, 'called function must be a function definition');
 			// only merge the environments they have in common
 			let environment = calledFn.environment;
 			while(environment.level > inputEnvironment.level) {

src/r-bridge/lang-4.x/ast/parser/json/format.ts

@@ -49,9 +49,9 @@ type ParsedDataRow = [line1: number, col1: number, line2: number, col2: number,
 export function prepareParsedData(data: string): CsvEntry[] {
 	let json: unknown;
 	try {
-		json = JSON.parse(`[${data}]`);
+		json = JSON.parse(`[${data.trim()}]`);
 	} catch(e) {
-		throw new Error(`Failed to parse data ${data}: ${(e as Error)?.message}`);
+		throw new Error(`Failed to parse data [${data}]: ${(e as Error)?.message}`);
 	}
 	guard(Array.isArray(json), () => `Expected ${data} to be an array but was not`);
 

src/reconstruct/reconstruct.ts

@@ -300,14 +300,14 @@ function reconstructArgument(argument: RArgument<ParentInformation>, name: Code
 }
 
 
-function reconstructParameter(parameter: RParameter<ParentInformation>, name: Code, defaultValue: unknown, configuration: ReconstructionConfiguration): Code {
+function reconstructParameter(parameter: RParameter<ParentInformation>, name: Code, defaultValue: Code | undefined, configuration: ReconstructionConfiguration): Code {
 	if(isSelected(configuration, parameter)) {
 		return plain(getLexeme(parameter));
 	}
 	if(parameter.defaultValue !== undefined && name.length > 0) {
 		return plain(`${getLexeme(parameter.name)}=${getLexeme(parameter.defaultValue)}`);
 	} else if(parameter.defaultValue !== undefined && name.length === 0) {
-		return plain(getLexeme(parameter.defaultValue));
+		return defaultValue ?? [];
 	} else {
 		return name;
 	}

test/functionality/slicing/static-program-slices/calls.test.ts

@@ -538,6 +538,10 @@ y` /* the formatting here seems wild, why five spaces */, { expectedOutput: '[1]
 			shell, 'c <- 3\nc(1, 2, 3)', ['2@c'], 'c(1, 2, 3)');
 	});
 	describe('Failures in Practice', () => {
+		describe('empty functions', () => {
+			assertSliced(label('Empty Function in Reconstruct', ['function-definitions']), shell,
+				'x <- 2\nfoo <- function(n, x = 3) { print(x) }\nprint(x)', ['3@x'], 'x <- 2\nx');
+		});
 		describe('Inverted Caller', () => {
 			assertSliced(label('Call from Higher', ['function-calls', 'lexicographic-scope']),
 				shell, 'create <- function() function() 3\ng <- create()\nc <- g()', ['3@c'], 'create <- function() function() 3\ng <- create()\nc <- g()');