Mutalyzer py.test 因 python-magic 错误而失败

Question

我正在尝试按照these 说明使用Anaconda Python 2.7 在Centos 6.7 上安装mutalyzer 2.0.14。

我的安装很顺利，但是当我尝试运行 py.test 套件时出现一系列失败。

我怀疑操作系统的libmagic 和python2.7 包python-magic 之间存在版本冲突。

如果有人能解释这里发生了什么或者更好地建议解决这个问题，我会非常感兴趣。

我的 libmagic 安装：

$ rpm -qa | grep 'file-'
file-libs-5.04-21.el6.x86_64
file-5.04-21.el6.x86_64
file-devel-5.04-21.el6.x86_64

对应的Python包：

$ source activate  py27
discarding /opt/anaconda2/bin from PATH
prepending /opt/anaconda2/envs/py27/bin to PATH
(py27) $ pip list | grep magic 
Magic-file-extensions (0.2, /home/chris.guest/temp/mutalyzer/src/magic-file-extensions)
python-magic (0.4.10)

py.test 是这样开始的：

# py.test
======================================================= test session starts =======================================================
platform linux2 -- Python 2.7.11, pytest-2.8.2, py-1.4.30, pluggy-0.3.1
rootdir: /home/chris.guest/temp/mutalyzer, inifile: 
collected 610 items / 3 errors 

tests/test_backtranslator.py ......
tests/test_base.py .
tests/test_crossmap.py .......................
tests/test_grammar.py ........................................................................................
tests/test_mapping.py ..............................
tests/test_migrations.py .
tests/test_mutator.py ................................................................................................................................................................
tests/test_ncbi.py ............................................................................................................
tests/test_parsers_genbank.py ..........

并以很多错误结束。由于undefined symbol: magic_list，许多测试失败：

_________________________________________ ERROR at setup of test_batch_unicode[sqlite://] _________________________________________

    @pytest.fixture
    def website():
>       return create_app().test_client()

tests/test_website.py:29: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
mutalyzer/website/__init__.py:35: in create_app
    from mutalyzer.website.views import website
mutalyzer/website/views.py:26: in <module>
    from mutalyzer import (announce, backtranslator, File, Retriever, Scheduler,
mutalyzer/File.py:23: in <module>
    import magic           # open(), MAGIC_MIME, MAGIC_NONE
src/magic-file-extensions/magic.py:94: in <module>
    _list = _libraries['magic'].magic_list
/opt/anaconda2/envs/py27/lib/python2.7/ctypes/__init__.py:378: in __getattr__
    func = self.__getitem__(name)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <CDLL 'libmagic.so.1', handle 160cc50 at 7f23b97340d0>, name_or_ordinal = 'magic_list'

    def __getitem__(self, name_or_ordinal):
>       func = self._FuncPtr((name_or_ordinal, self))
E       AttributeError: /usr/lib64/libmagic.so.1: undefined symbol: magic_list

/opt/anaconda2/envs/py27/lib/python2.7/ctypes/__init__.py:383: AttributeError
______________________________________ ERROR at setup of test_batch_unicode_email[sqlite://] ______________________________________

    @pytest.fixture
    def website():
>       return create_app().test_client()

tests/test_website.py:29: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
mutalyzer/website/__init__.py:35: in create_app
    from mutalyzer.website.views import website
mutalyzer/website/views.py:26: in <module>
    from mutalyzer import (announce, backtranslator, File, Retriever, Scheduler,
mutalyzer/File.py:23: in <module>
    import magic           # open(), MAGIC_MIME, MAGIC_NONE
src/magic-file-extensions/magic.py:94: in <module>
    _list = _libraries['magic'].magic_list
/opt/anaconda2/envs/py27/lib/python2.7/ctypes/__init__.py:378: in __getattr__
    func = self.__getitem__(name)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <CDLL 'libmagic.so.1', handle 160cc50 at 7f23b984ef50>, name_or_ordinal = 'magic_list'

    def __getitem__(self, name_or_ordinal):
>       func = self._FuncPtr((name_or_ordinal, self))
E       AttributeError: /usr/lib64/libmagic.so.1: undefined symbol: magic_list

/opt/anaconda2/envs/py27/lib/python2.7/ctypes/__init__.py:383: AttributeError
============================================== 548 passed, 65 error in 41.42 seconds ==============================================
(py27)[root@localhost mutalyzer]# 

Answer 1

我们之前有一份报告称，一位用户试图在 CentOS 6 上安装 Mutalyzer，但他们也遇到了 libmagic 的问题。除了他们切换到 CentOS 7 之外，我认为这没有得到解决。

不幸的是，我们的资源非常有限，而 Debian 是我们自己使用的唯一操作系统，这是我们可以实际支持的全部。当然，我们很乐意接受补丁或文档更新 :)

感谢您使用 Mutalyzer！

Answer 2

Centos 6.7 打包的magiclib 版本缺少magic_list 函数。

我能够将这个补丁添加到src/magic-file-extensions/magic.py，以便 py.test 可以正常运行。

$ diff -u src/magic-file-extensions/magic.old.py src/magic-file-extensions/magic.py
--- src/magic-file-extensions/magic.old.py  2015-12-31 14:04:50.769635453 +1100
+++ src/magic-file-extensions/magic.py  2016-01-11 15:17:49.987270845 +1100
@@ -91,9 +91,13 @@
 _check.restype = c_int
 _check.argtypes = [magic_t, c_char_p]

-_list = _libraries['magic'].magic_list
-_list.restype = c_int
-_list.argtypes = [magic_t, c_char_p]
+try:
+    _list = _libraries['magic'].magic_list
+    _list.restype = c_int
+    _list.argtypes = [magic_t, c_char_p]
+except AttributeError, e:
+    _list = None
+    

 _errno = _libraries['magic'].magic_errno
 _errno.restype = c_int

虽然使用此补丁处理直接的AttributeError，但如果调用src/magic-file-extensions/magic.py 中的Magic.list 方法，它仍然会失败。这不是一个直接的问题，因为它似乎没有在 mutalyzer 代码库中被调用。