Merge pull request #424 from biothings/tar-file-handling

Tar file handling

Author: shuchenliu

biothings/utils/common.py

@@ -21,6 +21,7 @@
 import random
 import string
 import sys
+import tarfile
 import time
 import types
 import urllib.parse
@@ -160,7 +161,7 @@ def safewfile(filename, prompt=True, default="C", mode="w"):
 
 def anyfile(infile, mode="r"):
     """
-    return a file handler with the support for gzip/zip comppressed files.
+    return a file handler with the support for gzip/zip compressed files.
     if infile is a two value tuple, then first one is the compressed file;
     the second one is the actual filename in the compressed file.
     e.g., ('a.zip', 'aa.txt')
@@ -171,6 +172,25 @@ def anyfile(infile, mode="r"):
     else:
         rawfile = os.path.splitext(infile)[0]
     filetype = os.path.splitext(infile)[1].lower()
+
+
+    # use tarfile built-in method to check for tar file before anything else
+    if tarfile.is_tarfile(infile):
+        tar_file = tarfile.open(infile, mode)
+        try:
+            extracted = tar_file.extractfile(rawfile)
+        except KeyError:
+            # provided rawfile does not appear in the tarball
+            tar_file.close()
+            raise Exception("target member does not contain the provided tar file.")
+
+        # extracted member is not a regular file or link
+        if extracted is None:
+            tar_file.close()
+            raise Exception("invalid target file: must be a regular file or a link")
+
+        return io.TextIOWrapper(extracted)
+
     if filetype == ".gz":
         # import gzip
         in_f = io.TextIOWrapper(gzip.GzipFile(infile, mode))