fix(r): setMethod emits call edge, not duplicate definition

crates/codegraph-core/src/extractors/r_lang.rs

@@ -163,10 +163,14 @@ fn handle_call(node: &Node, source: &[u8], symbols: &mut FileSymbols) {
                 handle_set_class(node, source, symbols);
                 return;
             }
-            "setGeneric" | "setMethod" => {
+            "setGeneric" => {
                 handle_set_generic(node, source, symbols);
                 return;
             }
+            "setMethod" => {
+                handle_set_method(node, source, symbols);
+                return;
+            }
             _ => {}
         }
     }
@@ -332,6 +336,23 @@ fn handle_set_generic(node: &Node, source: &[u8], symbols: &mut FileSymbols) {
     }
 }
 
+// `setMethod("greet", "Person", function(x) ...)` registers an implementation
+// of the generic `greet` — it is not a new top-level definition. Emitting a
+// definition here produced two `function` nodes with the same name (one from
+// setGeneric, one from setMethod) and broke resolution. Emit a call edge to
+// the generic instead; the method body's calls are still picked up by the
+// recursive walk of the anonymous function argument.
+fn handle_set_method(node: &Node, source: &[u8], symbols: &mut FileSymbols) {
+    if let Some(name) = first_argument_value(node, source, false) {
+        symbols.calls.push(Call {
+            name,
+            line: start_line(node),
+            dynamic: None,
+            receiver: None,
+        });
+    }
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -439,6 +460,51 @@ mod tests {
         assert_eq!(d.kind, "function");
     }
 
+    #[test]
+    fn set_method_does_not_duplicate_generic_definition() {
+        // Idiomatic S4: a setGeneric followed by setMethod implementations.
+        // Only the setGeneric should emit a definition — setMethod registers
+        // an implementation of the generic, which we model as a call edge.
+        let code = r#"
+setGeneric("greet", function(x) standardGeneric("greet"))
+setMethod("greet", "Person", function(x) paste("Hello", x@name))
+setMethod("greet", "Animal", function(x) paste("Hi", x@species))
+"#;
+        let s = parse_r(code);
+        let greet_defs: Vec<&Definition> =
+            s.definitions.iter().filter(|d| d.name == "greet").collect();
+        assert_eq!(
+            greet_defs.len(),
+            1,
+            "expected exactly one `greet` definition, got {greet_defs:#?}",
+        );
+        assert_eq!(greet_defs[0].kind, "function");
+    }
+
+    #[test]
+    fn set_method_emits_call_to_generic() {
+        // setMethod registers an implementation of the generic. The fix emits
+        // a call edge to the generic so the dispatch relationship is visible
+        // in the graph.
+        let s = parse_r(
+            "setMethod(\"greet\", \"Person\", function(x) paste(\"Hello\", x@name))\n",
+        );
+        let calls: Vec<&Call> = s.calls.iter().filter(|c| c.name == "greet").collect();
+        assert_eq!(calls.len(), 1, "expected setMethod to emit one call to `greet`");
+    }
+
+    #[test]
+    fn set_method_body_calls_are_still_captured() {
+        // The recursive walk visits the anonymous function passed to
+        // setMethod, so calls inside the method body must still appear.
+        let s = parse_r(
+            "setMethod(\"greet\", \"Person\", function(x) { helper(x); validate(x) })\n",
+        );
+        let names: Vec<&str> = s.calls.iter().map(|c| c.name.as_str()).collect();
+        assert!(names.contains(&"helper"), "method body call `helper` not captured");
+        assert!(names.contains(&"validate"), "method body call `validate` not captured");
+    }
+
     #[test]
     fn function_with_double_arrow_assignment() {
         // `<<-` is super-assignment in R; the JS extractor accepts it too.

src/extractors/r.ts

@@ -125,11 +125,16 @@ function handleCall(node: TreeSitterNode, ctx: ExtractorOutput): void {
     return;
   }
 
-  if (funcName === 'setGeneric' || funcName === 'setMethod') {
+  if (funcName === 'setGeneric') {
     handleSetGeneric(node, ctx);
     return;
   }
 
+  if (funcName === 'setMethod') {
+    handleSetMethod(node, ctx);
+    return;
+  }
+
   // Regular call
   if (funcNode.type === 'identifier') {
     ctx.calls.push({ name: funcName, line: node.startPosition.row + 1 });
@@ -212,63 +217,77 @@ function handleLibraryCall(node: TreeSitterNode, ctx: ExtractorOutput): void {
 }
 
 function handleSourceCall(node: TreeSitterNode, ctx: ExtractorOutput): void {
-  for (let i = 0; i < node.childCount; i++) {
-    const child = node.child(i);
-    if (!child || child.type !== 'arguments') continue;
-    for (let j = 0; j < child.childCount; j++) {
-      const arg = child.child(j);
-      if (!arg) continue;
-      if (arg.type === 'string') {
-        const text = arg.text.replace(/^["']|["']$/g, '');
-        ctx.imports.push({
-          source: text,
-          names: ['source'],
-          line: node.startPosition.row + 1,
-        });
-        return;
-      }
-    }
-  }
+  // source() only accepts string literals — `source(varname)` is not an import.
+  const path = firstStringArgument(node);
+  if (path === null) return;
+  ctx.imports.push({
+    source: path,
+    names: ['source'],
+    line: node.startPosition.row + 1,
+  });
 }
 
 function handleSetClass(node: TreeSitterNode, ctx: ExtractorOutput): void {
-  for (let i = 0; i < node.childCount; i++) {
-    const child = node.child(i);
-    if (!child || child.type !== 'arguments') continue;
-    for (let j = 0; j < child.childCount; j++) {
-      const arg = child.child(j);
-      if (!arg) continue;
-      if (arg.type === 'string') {
-        const name = arg.text.replace(/^["']|["']$/g, '');
-        ctx.definitions.push({
-          name,
-          kind: 'class',
-          line: node.startPosition.row + 1,
-          endLine: nodeEndLine(node),
-        });
-        return;
-      }
-    }
-  }
+  const name = firstStringArgument(node);
+  if (name === null) return;
+  ctx.definitions.push({
+    name,
+    kind: 'class',
+    line: node.startPosition.row + 1,
+    endLine: nodeEndLine(node),
+  });
 }
 
 function handleSetGeneric(node: TreeSitterNode, ctx: ExtractorOutput): void {
+  const name = firstStringArgument(node);
+  if (name === null) return;
+  ctx.definitions.push({
+    name,
+    kind: 'function',
+    line: node.startPosition.row + 1,
+    endLine: nodeEndLine(node),
+  });
+}
+
+// setMethod("greet", "Person", function(x) ...) registers an implementation of
+// the generic `greet` — it is not a new top-level definition. Emitting a
+// definition here produced two `function` nodes with the same name (one from
+// setGeneric, one from setMethod) and broke resolution. Emit a call edge to
+// the generic instead; the method body's calls are still picked up by the
+// recursive walk of the anonymous function argument.
+function handleSetMethod(node: TreeSitterNode, ctx: ExtractorOutput): void {
+  const name = firstStringArgument(node);
+  if (name === null) return;
+  ctx.calls.push({ name, line: node.startPosition.row + 1 });
+}
+
+// tree-sitter-r wraps each positional argument in an `argument` node that
+// contains the actual `string` (or `identifier`) child, so the inner string
+// must be unwrapped — checking `child.type === 'string'` directly misses it.
+// Mirrors `first_argument_value` in the Rust extractor for parity.
+function firstStringArgument(node: TreeSitterNode): string | null {
   for (let i = 0; i < node.childCount; i++) {
     const child = node.child(i);
     if (!child || child.type !== 'arguments') continue;
     for (let j = 0; j < child.childCount; j++) {
       const arg = child.child(j);
       if (!arg) continue;
       if (arg.type === 'string') {
-        const name = arg.text.replace(/^["']|["']$/g, '');
-        ctx.definitions.push({
-          name,
-          kind: 'function',
-          line: node.startPosition.row + 1,
-          endLine: nodeEndLine(node),
-        });
-        return;
+        return stripQuotes(arg.text);
+      }
+      if (arg.type === 'argument') {
+        const valueNode = arg.childForFieldName('value');
+        if (valueNode && valueNode.type === 'string') return stripQuotes(valueNode.text);
+        for (let k = 0; k < arg.childCount; k++) {
+          const inner = arg.child(k);
+          if (inner && inner.type === 'string') return stripQuotes(inner.text);
+        }
       }
     }
   }
+  return null;
+}
+
+function stripQuotes(text: string): string {
+  return text.replace(/^["']|["']$/g, '');
 }

tests/parsers/r.test.ts

@@ -53,4 +53,61 @@ mean(c(1, 2, 3))`);
     expect(symbols.imports).toContainEqual(expect.objectContaining({ source: 'dplyr' }));
     expect(symbols.imports.some((i) => i.source === 'package')).toBe(false);
   });
+
+  it('extracts source() imports', () => {
+    // Parity guard: native produces an import with `source: "service.R"`.
+    // The WASM extractor previously failed silently for the same reason as
+    // setClass/setGeneric — it didn't unwrap the `argument` node.
+    const symbols = parseR(`source("service.R")`);
+    expect(symbols.imports).toContainEqual(
+      expect.objectContaining({ source: 'service.R', names: ['source'] }),
+    );
+  });
+
+  it('extracts a class definition from setClass', () => {
+    // Parity guard: the native extractor produces a `class` definition for
+    // `setClass(...)`; the WASM extractor previously failed silently because
+    // it did not unwrap the `argument` node around the string literal.
+    const symbols = parseR(`setClass("Person", representation(name = "character"))`);
+    expect(symbols.definitions).toContainEqual(
+      expect.objectContaining({ name: 'Person', kind: 'class' }),
+    );
+  });
+
+  it('extracts a function definition from setGeneric', () => {
+    // Same parity guard for setGeneric — was silently broken in WASM.
+    const symbols = parseR(`setGeneric("doIt", function(x) standardGeneric("doIt"))`);
+    expect(symbols.definitions).toContainEqual(
+      expect.objectContaining({ name: 'doIt', kind: 'function' }),
+    );
+  });
+
+  it('does not duplicate the generic definition when setMethod is present', () => {
+    // Idiomatic S4: a setGeneric followed by setMethod implementations.
+    // Only setGeneric should emit a function definition — setMethod registers
+    // an implementation, which we model as a call edge to the generic.
+    const symbols = parseR(`
+setGeneric("greet", function(x) standardGeneric("greet"))
+setMethod("greet", "Person", function(x) paste("Hello", x@name))
+setMethod("greet", "Animal", function(x) paste("Hi", x@species))
+`);
+    const greetDefs = symbols.definitions.filter((d) => d.name === 'greet');
+    expect(greetDefs).toHaveLength(1);
+    expect(greetDefs[0]).toMatchObject({ kind: 'function' });
+  });
+
+  it('emits a call to the generic for setMethod', () => {
+    const symbols = parseR(`setMethod("greet", "Person", function(x) paste("Hello", x@name))`);
+    const greetCalls = symbols.calls.filter((c) => c.name === 'greet');
+    expect(greetCalls).toHaveLength(1);
+  });
+
+  it('still captures calls from inside the setMethod body', () => {
+    // The recursive walk visits the anonymous function passed to setMethod,
+    // so calls inside the method body must still appear in ctx.calls.
+    const symbols = parseR(`setMethod("greet", "Person", function(x) { helper(x); validate(x) })`);
+    const names = symbols.calls.map((c) => c.name);
+    expect(names).toContain('helper');
+    expect(names).toContain('validate');
+  });
 });