From 43b0b4f6671395b039533e588178cc65e645e96a Mon Sep 17 00:00:00 2001
From: mgiulini <mrcgiulini@gmail.com>
Date: Wed, 11 Dec 2024 15:14:47 +0100
Subject: [PATCH] added flat tar extraction

---
 src/haddock/gear/clean_steps.py |  4 ++--
 src/haddock/gear/prepare_run.py |  5 ++---
 src/haddock/libs/libio.py       | 23 +++++++++++++++++++++++
 3 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/src/haddock/gear/clean_steps.py b/src/haddock/gear/clean_steps.py
index a73915d6f..933412d49 100644
--- a/src/haddock/gear/clean_steps.py
+++ b/src/haddock/gear/clean_steps.py
@@ -163,8 +163,8 @@ def unpack_compressed_and_archived_files(folders: Iterable[FilePathT],
                     pass
 
         for tar_file in tar_files:
-            with tarfile.open(tar_file) as fin:
-                fin.extractall(folder)
+            from haddock.libs.libio import extract_files_flat
+            extract_files_flat(tar_file, folder)
 
             tar_file.unlink()
 
diff --git a/src/haddock/gear/prepare_run.py b/src/haddock/gear/prepare_run.py
index 65b03cbb8..8f1ee274b 100644
--- a/src/haddock/gear/prepare_run.py
+++ b/src/haddock/gear/prepare_run.py
@@ -70,7 +70,7 @@
     )
 from haddock.gear.zerofill import zero_fill
 from haddock.libs.libfunc import not_none
-from haddock.libs.libio import make_writeable_recursive
+from haddock.libs.libio import make_writeable_recursive, extract_files_flat
 from haddock.libs.libutil import (
     extract_keys_recursive,
     recursive_convert_paths_to_strings,
@@ -1040,8 +1040,7 @@ def copy_input_files_to_data_dir(
                     # account for input .tgz files
                     if name.endswith("tgz"):
                         log.info(f"Uncompressing tar {value}")
-                        with tarfile.open(target_path) as fin:
-                            fin.extractall(pf)
+                        extract_files_flat(value, pf)
 
 
 def check_run_dir_exists(run_dir: FilePath) -> None:
diff --git a/src/haddock/libs/libio.py b/src/haddock/libs/libio.py
index 05e317a27..8f0b17c77 100644
--- a/src/haddock/libs/libio.py
+++ b/src/haddock/libs/libio.py
@@ -21,6 +21,7 @@
     Iterable,
     Mapping,
     Optional,
+    Union,
     )
 from haddock.libs.libontology import PDBFile
 from haddock.libs.libutil import sort_numbered_paths
@@ -613,3 +614,25 @@ def make_writeable_recursive(path: FilePath) -> None:
 
         for file_ in (os.path.join(root, f) for f in files):
             os.chmod(file_, get_perm(file_) | stat.S_IWUSR)
+
+
+def extract_files_flat(tar_path: Union[str, FilePath],
+                       dest_path: Union[str, FilePath]) -> None:
+    """
+    Extract files from a tarball to a destination folder.
+    
+    Parameters
+    ----------
+    tar_path : str or Path
+        The path to the tarball file.
+
+    dest_path : str or Path
+        The path to the destination folder.
+    """
+    with tarfile.open(tar_path, "r:gz") as tar:
+        for member in tar.getmembers():
+            # Extract only files (skip directories)
+            if member.isfile():
+                # Modify the member name to remove the directory structure
+                member.name = os.path.basename(member.name)
+                tar.extract(member, dest_path)