CVE-2007-4559 Patch

transformers/transformers/trj_correlated_motions_transformer.py

@@ -394,7 +394,26 @@ def process(structure_dict):
         trj_dir = trjtar
     elif tarfile.is_tarfile(trjtar):
         with tarfile.open(name=trjtar, mode='r:gz') as tfile:
-            tfile.extractall()
+            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(tfile)
             logger.info('extracting frameset')
             trj_dir = tfile.getnames()[0]
     else:

transformers/transformers/trj_hbond_transformer.py

@@ -479,7 +479,26 @@ def _process(structure_dict):
         trj_dir = trjtar
     elif tarfile.is_tarfile(trjtar):
         with tarfile.open(name=trjtar, mode='r:gz') as tfile:
-            tfile.extractall()
+            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(tfile)
             logger.info('extracting frameset')
             trj_dir = tfile.getnames()[0]
     else:

transformers/transformers/trj_mmgbsa_transformer.py

@@ -169,7 +169,26 @@ def _process(structure_dict):
         trj_dir = trjtar
     elif tarfile.is_tarfile(trjtar):
         with tarfile.open(name=trjtar, mode='r:gz') as tfile:
-            tfile.extractall()
+            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(tfile)
             logger.info('extracting frameset')
             trj_dir = tfile.getnames()[0]
     else:

transformers/transformers/trj_nonbonded_transformer.py

@@ -652,7 +652,26 @@ def _process(structure_dict):
         trj_dir = trjtar
     elif tarfile.is_tarfile(trjtar):
         with tarfile.open(name=trjtar, mode='r:gz') as tfile:
-            tfile.extractall()
+            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(tfile)
             logger.info('extracting frameset')
             trj_dir = tfile.getnames()[0]
     else:
@@ -687,7 +706,26 @@ def _process(structure_dict):
             with tarfile.open(nonbonded_raw, 'r:bz2') as tar:
                 if not os.path.isdir('./tmp'):
                     os.mkdir('./tmp')
-                tar.extractall(path='./tmp')
+                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="./tmp")
                 members = tar.getmembers()
             with tarfile.open(outfile_raw, 'w:bz2') as tar:
                 for member in members:

transformers/transformers/trj_rms_transformer.py

@@ -262,7 +262,26 @@ def _process(structure_dict):
         trj_dir = trjtar
     elif tarfile.is_tarfile(trjtar):
         with tarfile.open(name=trjtar, mode='r:gz') as tfile:
-            tfile.extractall()
+            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(tfile)
             logger.info('extracting frameset')
             trj_dir = tfile.getnames()[0]
     else:

transformers/transformers/trj_torsion_transformer.py

@@ -288,7 +288,26 @@ def _process(structure_dict):
         trj_dir = trjtar
     elif tarfile.is_tarfile(trjtar):
         with tarfile.open(name=trjtar, mode='r:gz') as tfile:
-            tfile.extractall()
+            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(tfile)
             trj_dir = tfile.getnames()[0]
     else:
         raise RuntimeError('trjtar is neither a directory nor a tarfile')

transformers/transformers/trj_water_contacts_transformer.py

@@ -216,7 +216,26 @@ def _process(structure_dict):
         trj_dir = trjtar
     elif tarfile.is_tarfile(trjtar):
         with tarfile.open(name=trjtar, mode='r:gz') as tfile:
-            tfile.extractall()
+            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(tfile)
             logger.info('extracting frameset')
             trj_dir = tfile.getnames()[0]
     else:

transformers/utils/preprocess.py

@@ -526,7 +526,26 @@ def preprocess_torsion(api, dataset, data_type=None, no_ligand=False):
                 trj_torsion = get_trj_torsion(api, stid, dir=tempdir)
 
             with tarfile.open(trj_torsion, 'r:gz') as tar:
-                tar.extractall(path=tempdir)
+                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=tempdir)
 
             torsion_ids = pd.read_csv('torsion_ids.csv', sep=',', index_col=0)
             for tid in torsion_ids.index: