Merge pull request #416 from drdavella/asdf-fits-gzip

Fix bug when reading gzipped ASDF-in-FITS file

CHANGES.rst

@@ -10,6 +10,9 @@
 1.4.0 (unreleased)
 ------------------
 
+- Improve the way URIs are detected for ASDF-in-FITS files in order to fix bug
+  with reading gzipped ASDF-in-FITS files. [#416]
+
 - Explicitly disallow access to entire tree for ASDF file objects that have
   been closed. [#407]
 

asdf/fits_embed.py

@@ -192,17 +192,15 @@ def open(cls, fd, uri=None, validate_checksums=False, extensions=None,
         if isinstance(fd, fits.hdu.hdulist.HDUList):
             hdulist = fd
         else:
-            file_obj = generic_io.get_file(fd, uri=uri)
-            uri = file_obj._uri if uri is None and file_obj._uri else ''
+            uri = generic_io.get_uri(fd)
             try:
-                hdulist = fits.open(file_obj)
+                hdulist = fits.open(fd)
                 # Since we created this HDUList object, we need to be
                 # responsible for cleaning up upon close() or __exit__
                 close_hdulist = True
             except IOError:
-                file_obj.close()
                 msg = "Failed to parse given file '{}'. Is it FITS?"
-                raise ValueError(msg.format(file_obj.uri))
+                raise ValueError(msg.format(uri))
 
         self = cls(hdulist, uri=uri, extensions=extensions,
                    ignore_version_mismatch=ignore_version_mismatch,

asdf/generic_io.py

@@ -32,7 +32,7 @@
 from .extern import atomicfile
 
 
-__all__ = ['get_file', 'resolve_uri', 'relative_uri']
+__all__ = ['get_file', 'get_uri', 'resolve_uri', 'relative_uri']
 
 
 _local_file_schemes = ['', 'file']
@@ -1083,6 +1083,22 @@ def _make_http_connection(init, mode, uri=None):
     return HTTPConnection(connection, size, parsed.path, uri or init,
                           first_chunk)
 
+def get_uri(file_obj):
+    """
+    Returns the uri of the given file object
+
+    Parameters
+    ----------
+    uri : object
+    """
+    if isinstance(file_obj, six.string_types):
+        return file_obj
+    if isinstance(file_obj, GenericFile):
+        return file_obj.uri
+
+    # A catch-all for types from Python's io module that have names
+    return getattr(file_obj, 'name', '')
+
 
 def get_file(init, mode='r', uri=None):
     """

asdf/tests/setup_package.py

@@ -6,4 +6,4 @@
 def get_package_data():  # pragma: no cover
     return {
         str(_PACKAGE_NAME_ + '.tests'):
-            ['coveragerc', 'data/*.yaml', 'data/*.json', 'data/*.fits']}
+            ['coveragerc', 'data/*.yaml', 'data/*.json', 'data/*.fits', 'data/*.fits.gz']}

asdf/tests/test_fits_embed.py

@@ -214,6 +214,20 @@ def test_asdf_open(tmpdir):
         with asdf_open(hdulist) as ff:
             compare_asdfs(asdf_in_fits, ff)
 
+def test_open_gzipped():
+    testfile = os.path.join(TEST_DATA_PATH, 'asdf.fits.gz')
+
+    # Opening as an HDU should work
+    with fits.open(testfile) as ff:
+        with asdf.AsdfFile.open(ff) as af:
+            assert af.tree['stuff'].shape == (20, 20)
+
+    with fits_embed.AsdfInFits.open(testfile) as af:
+        assert af.tree['stuff'].shape == (20, 20)
+
+    with asdf.AsdfFile.open(testfile) as af:
+        assert af.tree['stuff'].shape == (20, 20)
+
 def test_bad_input(tmpdir):
     """Make sure these functions behave properly with bad input"""
     text_file = os.path.join(str(tmpdir), 'test.txt')
@@ -237,7 +251,7 @@ def test_version_mismatch_file():
     assert len(w) == 1
     assert str(w[0].message) == (
         "'tag:stsci.edu:asdf/core/complex' with version 7.0.0 found in file "
-        "'file://{}', but latest supported version is 1.0.0".format(testfile))
+        "'{}', but latest supported version is 1.0.0".format(testfile))
 
     # Make sure warning does not occur when warning is ignored (default)
     with catch_warnings() as w:
@@ -252,7 +266,7 @@ def test_version_mismatch_file():
     assert len(w) == 1
     assert str(w[0].message) == (
         "'tag:stsci.edu:asdf/core/complex' with version 7.0.0 found in file "
-        "'file://{}', but latest supported version is 1.0.0".format(testfile))
+        "'{}', but latest supported version is 1.0.0".format(testfile))
 
     # Make sure warning does not occur when warning is ignored (default)
     with catch_warnings() as w: