CVE-2007-4559 Patch

MDAnalysisData/adk_transitions.py

@@ -174,7 +174,29 @@ def _fetch_adk_transitions(metadata, data_home=None, download_if_missing=True):
 
         logger.info("Unpacking {}...".format(archive_path))
         with tarfile.open(archive_path, 'r') as tar:
-            tar.extractall(path=data_location)
+
+            import os
+
+            def is_within_directory(directory, target):
+
+                abs_directory = os.path.abspath(directory)
+                abs_target = os.path.abspath(target)
+
+                prefix = os.path.commonprefix([abs_directory, abs_target])
+
+                return prefix == abs_directory
+
+            def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
+
+                for member in tar.getmembers():
+                    member_path = os.path.join(path, member.name)
+                    if not is_within_directory(path, member_path):
+                        raise Exception("Attempted Path Traversal in Tar File")
+
+                tar.extractall(path, members, numeric_owner=numeric_owner) 
+
+
+            safe_extract(tar, path=data_location)
 
     records.topology = join(data_location, metadata['CONTENTS']['topology'])
     if not exists(records.topology):

MDAnalysisData/vesicles.py

@@ -92,7 +92,29 @@ def fetch_vesicle_lib(data_home=None, download_if_missing=True):
 
         logger.info("Unpacking {}...".format(archive_path))
         with tarfile.open(archive_path, 'r') as tar:
-            tar.extractall(path=data_location)
+
+            import os
+
+            def is_within_directory(directory, target):
+
+                abs_directory = os.path.abspath(directory)
+                abs_target = os.path.abspath(target)
+
+                prefix = os.path.commonprefix([abs_directory, abs_target])
+
+                return prefix == abs_directory
+
+            def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
+
+                for member in tar.getmembers():
+                    member_path = os.path.join(path, member.name)
+                    if not is_within_directory(path, member_path):
+                        raise Exception("Attempted Path Traversal in Tar File")
+
+                tar.extractall(path, members, numeric_owner=numeric_owner) 
+
+
+            safe_extract(tar, path=data_location)
 
     records.structures = [join(data_location, path) for path in metadata['CONTENTS']['structures']
                           if exists(join(data_location, path))]