fix no file bugs

Author: Xu

rdagent/scenarios/data_science/dev/runner/__init__.py

@@ -113,7 +113,10 @@ def implement_one_task(
             queried_former_failed_knowledge=queried_former_failed_knowledge[0],
         )
         code = session.build_chat_completion(user_prompt=user_prompt)
-        code_batch_edit = extract_output_fn(code)
+        if self.settings.diff_mode:
+            code_batch_edit = extract_output_fn(code, prefix=workspace.workspace_path)
+        else:
+            code_batch_edit = extract_output_fn(code)
         code_batch_edit = {k: v for k, v in code_batch_edit.items() if k in workspace.file_dict.keys()}
 
         # Change Summary

rdagent/utils/agent/apply_patch.py

@@ -417,17 +417,26 @@ def text_to_patch(text: str, orig: dict[str, str]) -> tuple[Patch, int]:
     return parser.patch, parser.fuzz
 
 
-def identify_files_needed(text: str) -> list[str]:
+def identify_files_needed(text: str, prefix: str | None = None) -> list[str]:
     lines = text.splitlines()
-    return [line[len("*** Update File: ") :] for line in lines if line.startswith("*** Update File: ")] + [
-        line[len("*** Delete File: ") :] for line in lines if line.startswith("*** Delete File: ")
-    ]
+    update_files = [line[len("*** Update File: "):] for line in lines if line.startswith("*** Update File: ")]
+    delete_files = [line[len("*** Delete File: "):] for line in lines if line.startswith("*** Delete File: ")]
+    all_files = update_files + delete_files
+    
+    if prefix is None:
+        return all_files
+    else:
+        return [f"{prefix}/{file}" if prefix else file for file in all_files]
 
 
-def identify_files_added(text: str) -> list[str]:
+def identify_files_added(text: str, prefix: str | None = None) -> list[str]:
     lines = text.splitlines()
-    return [line[len("*** Add File: ") :] for line in lines if line.startswith("*** Add File: ")]
-
+    added_files = [line[len("*** Add File: "):] for line in lines if line.startswith("*** Add File: ")]
+    
+    if prefix is None:
+        return added_files
+    else:
+        return [f"{prefix}/{file}" if prefix else file for file in added_files]
 
 # --------------------------------------------------------------------------- #
 #  File-system helpers
@@ -468,10 +477,11 @@ def process_patch(
     write_fn: Callable[[str, str], None],
     remove_fn: Callable[[str], None],
     inplace: bool = False,
+    prefix: str | None = None
 ) -> str:
     if not text.startswith("*** Begin Patch"):
         raise DiffError("Patch text must start with *** Begin Patch")
-    paths = identify_files_needed(text)
+    paths = identify_files_needed(text, prefix)
     orig = load_files(paths, open_fn)
     patch, _fuzz = text_to_patch(text, orig)
     commit = patch_to_commit(patch, orig)
@@ -501,13 +511,13 @@ def remove_file(path: str) -> None:
 # --------------------------------------------------------------------------- #
 #  CLI entry-point
 # --------------------------------------------------------------------------- #
-def apply_patch_from_text(patch_text: str, inplace: bool = False) -> str:
+def apply_patch_from_text(patch_text: str, inplace: bool = False, prefix: str | None = None) -> str:
     """Apply patch text to filesystem, same as main() but with parameter input"""
     if not patch_text:
         raise DiffError("Patch text cannot be empty")
 
     try:
-        result = process_patch(patch_text, open_file, write_file, remove_file, inplace)
+        result = process_patch(patch_text, open_file, write_file, remove_file, inplace, prefix)
         return result
     except DiffError as exc:
         raise exc

rdagent/utils/agent/ret.py

@@ -91,12 +91,13 @@ def get_spec(cls):
         return T(".tpl:PythonBatchPatchOut").r()
 
     @classmethod
-    def extract_output(cls, resp: str) -> str:
+    def extract_output(cls, resp: str, prefix: str | None = None) -> str:
+        code_blocks = {}
         # Step 1: extract patch by pattern
         patch_pattern = re.compile(r"(\*\*\* Begin Patch\s*(.*?)\s*\*\*\* End Patch)", re.DOTALL)
-        match = patch_pattern.search(resp)
-        if match:
-            resp = match.group(1).rstrip()
+        matches = patch_pattern.findall(resp)
+        for match in matches:
+            code_blocks.update(apply_patch_from_text(match, inplace=False, prefix=prefix))
 
         # Step 2: apply the patch, this will modify the file in place
-        return apply_patch_from_text(resp, inplace=False)
+        return code_blocks