Merge pull request #1613 from erwanp/fix_gzip_not_found

remove call to system-wide gunzip. Use python version instead.

Author: bsipocz

astroquery/utils/system_tools.py

@@ -1,9 +1,7 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 from __future__ import print_function
-import subprocess
 import os
 
-
 # Import DEVNULL for py3 or py3
 try:
     from subprocess import DEVNULL
@@ -12,29 +10,6 @@
 
 # Check availability of some system tools
 # Exceptions are raised if not found
-__is_gzip_found = False
-for test_cmd in (["gzip", "-V"], ["7z"]):
-    try:
-        subprocess.call(test_cmd, stdout=DEVNULL, stderr=DEVNULL)
-    except OSError:
-        pass
-    else:
-        __is_gzip_found = test_cmd[0]
-
-
-if __is_gzip_found == 'gzip':
-    def _unzip_cmd(filename):
-        return ["gzip", "-d", "{0}".format(filename)]
-elif __is_gzip_found == '7z':
-    def _unzip_cmd(filename):
-        return ["7z", "x",
-                "{0}".format(filename),
-                "-o{0}".format(os.path.split(filename)[0])]
-else:
-    print("gzip was not found on your system! You should solve this issue for "
-          "astroquery.eso to be at its best!\n"
-          "On POSIX system: make sure gzip is installed and in your path!"
-          "On Windows: same for 7-zip (http://www.7-zip.org)!")
 
 
 def gunzip(filename):
@@ -50,9 +25,17 @@ def gunzip(filename):
         Name of the decompressed file (or input filename if gzip is not
         available).
     """
+    import shutil
+    import gzip
+
+    # system-wide 'gzip' was removed, Python gzip used instead.
+    # See #1538 : https://github.com/astropy/astroquery/issues/1538
+
     # ".fz" denotes RICE rather than gzip compression
-    if __is_gzip_found and not filename.endswith('.fz'):
-        subprocess.call(_unzip_cmd(filename), stdout=DEVNULL, stderr=DEVNULL)
+    if not filename.endswith('.fz'):
+        with gzip.open(filename, 'rb') as f_in:
+            with open(filename.rsplit(".", 1)[0], 'wb') as f_out:
+                shutil.copyfileobj(f_in, f_out)
         return filename.rsplit(".", 1)[0]
     else:
         return filename

astroquery/utils/tests/test_system_tools.py

@@ -0,0 +1,44 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+try:
+    import gzip
+
+    HAS_GZIP = True
+except ImportError:
+    HAS_GZIP = False
+
+import shutil
+import os
+from os.path import exists
+import tempfile
+
+import pytest
+
+from ..system_tools import gunzip
+
+
+@pytest.mark.skipif("not HAS_GZIP")
+def test_gunzip():
+
+    temp_dir = tempfile.mkdtemp()
+    filename = temp_dir + os.sep + "test_gunzip.txt.gz"
+    unziped_filename = filename.rsplit(".", 1)[0]
+
+    # First create a gzip file
+    content = b"Bla"
+    with gzip.open(filename, "wb") as f:
+        f.write(content)
+
+    try:
+        # Then test our gunzip command works and creates an unziped file
+        gunzip(filename)
+        assert exists(unziped_filename)
+
+        # Check content is the same
+        with open(unziped_filename, "rb") as f:
+            new_content = f.read()
+        assert new_content == content
+
+    finally:
+        # Clean
+        shutil.rmtree(temp_dir)