happens with 2.0.1-634-g82a261c
After the fixup #468 ran into another failure which I am not sure at which stage should be addressed, so decided just to report with details:
======================================================================
ERROR: test_surf_gifti (mvpa2.tests.test_surfing.SurfTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/tools.py", line 278, in newfunc
func(*(arg + (filename,)), **kw)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/tests/test_surfing.py", line 1104, in test_surf_gifti
surf.write(fn, s)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/support/nibabel/surf.py", line 2229, in write
surf_gifti.write(fn, s, overwrite=overwrite)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/support/nibabel/surf_gifti.py", line 256, in write
xml = to_xml(s, fn)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/support/nibabel/surf_gifti.py", line 219, in to_xml
xml = img.to_xml().encode('utf-8')
File "/home/yoh/proj/nipy/nipy-suite/nibabel/nibabel/gifti/gifti.py", line 680, in to_xml
""" + xml.XmlSerializable.to_xml(self, enc)
File "/home/yoh/proj/nipy/nipy-suite/nibabel/nibabel/xmlutils.py", line 30, in to_xml
return tostring(self._to_xml_element(), enc)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1126, in tostring
ElementTree(element).write(file, encoding, method=method)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 820, in write
serialize(write, self._root, encoding, qnames, namespaces)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 939, in _serialize_xml
_serialize_xml(write, e, encoding, qnames, None)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 932, in _serialize_xml
v = _escape_attrib(v, encoding)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1092, in _escape_attrib
_raise_serialization_error(text)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1052, in _raise_serialization_error
"cannot serialize %r (type %s)" % (text, type(text).__name__)
TypeError: cannot serialize 0 (type int)
which happens due to "rogue" ExternalFileOffset being an int, not serialized to str
899 def _serialize_xml(write, elem, encoding, qnames, namespaces):
900 tag = elem.tag
901 text = elem.text
902 if tag is Comment:
903 write("<!--%s-->" % _encode(text, encoding))
904 elif tag is ProcessingInstruction:
905 write("<?%s?>" % _encode(text, encoding))
(Pdb)
906 else:
907 tag = qnames[tag]
908 if tag is None:
909 if text:
910 write(_escape_cdata(text, encoding))
911 for e in elem:
912 _serialize_xml(write, e, encoding, qnames, None)
913 else:
914 write("<" + tag)
915 items = elem.items()
916 if items or namespaces:
(Pdb)
917 if namespaces:
918 for v, k in sorted(namespaces.items(),
919 key=lambda x: x[1]): # sort on prefix
920 if k:
921 k = ":" + k
922 write(" xmlns%s=\"%s\"" % (
923 k.encode(encoding),
924 _escape_attrib(v, encoding)
925 ))
926 for k, v in sorted(items): # lexical order
927 if isinstance(k, QName):
(Pdb)
928 k = k.text
929 if isinstance(v, QName):
930 v = qnames[v.text]
931 else:
932 -> v = _escape_attrib(v, encoding)
933 write(" %s=\"%s\"" % (qnames[k], v))
934 if text or len(elem):
935 write(">")
936 if text:
937 write(_escape_cdata(text, encoding))
938 for e in elem:
(Pdb) p elem
<Element 'DataArray' at 0x7fd24f50de90>
*(Pdb) p elem.tag
'DataArray'
*(Pdb) p elem.text
None
(Pdb) p namespaces
None
(Pdb) p items
[('Dimensionality', '2'), ('ExternalFileName', ''), ('Encoding', 'GZipBase64Binary'), ('DataType', 'NIFTI_TYPE_FLOAT32'), ('ArrayIndexingOrder', 'RowMajorOrder'), ('ExternalFileOffset', 0), ('Dim0', '4'), ('Dim1', '3'), ('Intent', 'NIFTI_INTENT_POINTSET'), ('Endian', 'LittleEndian')]
matthew-brett
commented
8 years ago
happens with 2.0.1-634-g82a261c After the fixup #468 ran into another failure which I am not sure at which stage should be addressed, so decided just to report with details:
which happens due to "rogue" ExternalFileOffset being an int, not serialized to str