SSL issue with pip pysbol package on Linux

[tim-tx]

Python 2 and 3 affected (2.7 and 3.6 tested).

Steps to reproduce:

$ pip install pysbol --user
$ python
>>> from sbol import *
>>> partshop = PartShop('https://synbiohub.org/public/igem')
>>> records = partshop.search('interlab')

Result:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/me/.local/lib/python3.6/site-packages/sbol/libsbol.py", line 8643, in search
    val = _libsbol.PartShop_search(self, *args)
RuntimeError: Attempt to validate online failed with Problem with the SSL CA cert (path? access rights?)

The above steps work against pysbol built manually from the libSBOL source.

[bbartley]

Hi Tim,

I've attempted to correct this issue by recompiling libpython with OpenSSL and deploying a new wheel.

At your convenience, please update to the new wheel and re-test with Python3.6.

$ pip install --user --upgrade

This should upgrade your package to pySBOL-2.3.0.post20-cp36-cp36m-manylinux1_x86_64.whl

[tim-tx]

Here is the result:

Python 3.6.6 (default, Jun 27 2018, 13:11:40) 
[GCC 8.1.1 20180531] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sbol
Traceback (most recent call last):
  File "/home/tsj/.local/lib/python3.6/site-packages/sbol/libsbol.py", line 19, in swig_import_helper
return importlib.import_module(mname)
  File "/usr/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 658, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 571, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 922, in create_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
ImportError: /home/tsj/.local/lib/python3.6/site-packages/sbol/_libsbol.so: undefined symbol: MD5_Init

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/tsj/.local/lib/python3.6/site-packages/sbol/__init__.py", line 6, in <module>
from sbol.sbol import *
  File "/home/tsj/.local/lib/python3.6/site-packages/sbol/sbol.py", line 17, in <module>
from .libsbol import *
  File "/home/tsj/.local/lib/python3.6/site-packages/sbol/libsbol.py", line 22, in <module>
_libsbol = swig_import_helper()
  File "/home/tsj/.local/lib/python3.6/site-packages/sbol/libsbol.py", line 21, in swig_import_helper
return importlib.import_module('_libsbol')
  File "/usr/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
ModuleNotFoundError: No module named '_libsbol'

[bbartley]

@tim-tx Hi Tim, I've made another attempt at building the Linux wheel with support for secure HTTP:

At your convenience, please update to the new wheel and test with Python3.6.

$ pip install --user --upgrade

This should upgrade your package to pySBOL-2.3.0.post21-cp36-cp36m-manylinux1_x86_64.whl

[tim-tx]

@bbartley Hi Bryan, I did the upgrade, though I seem to be running into the same issue:

$ python3.6 -m pip show pysbol
Name: pySBOL
Version: 2.3.0.post21
...

And then:

$ python3.6                 
Python 3.6.6 (default, Aug 26 2018, 01:20:38) 
[GCC 8.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from sbol import *
Traceback (most recent call last):
  File "/home/lab/.local/lib/python3.6/site-packages/sbol/libsbol.py", line 19, in swig_import_helper
return importlib.import_module(mname)
  File "/usr/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 658, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 571, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 922, in create_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
ImportError: /home/lab/.local/lib/python3.6/site-packages/sbol/_libsbol.so: undefined symbol: MD5_Init

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/lab/.local/lib/python3.6/site-packages/sbol/__init__.py", line 6, in <module>
from sbol.sbol import *
  File "/home/lab/.local/lib/python3.6/site-packages/sbol/sbol.py", line 17, in <module>
from .libsbol import *
  File "/home/lab/.local/lib/python3.6/site-packages/sbol/libsbol.py", line 22, in <module>
_libsbol = swig_import_helper()
  File "/home/lab/.local/lib/python3.6/site-packages/sbol/libsbol.py", line 21, in swig_import_helper
return importlib.import_module('_libsbol')
  File "/usr/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
ModuleNotFoundError: No module named '_libsbol'

[bbartley]

Hi, the latest version of pySBOL now has a workaround for this issue. Before sending a request to synbiohub, you can configure the certificate path for your Linux distribution, as follows:

Config.setOption('ca-path', path_to_ca_file)

Where path_to_ca_file is defined as follows for different Linux distros:
Debian/Ubuntu: "/etc/ssl/certs/ca-certificates.crt"
Fedora/RHEL: "/etc/pki/tls/certs/ca-bundle.crt"
OpenSUSE : "/var/lib/ca-certificates/ca-bundle.pem"

By default the certificate path is configured for Red Hat Linux

[tim-tx]

Can you deploy a Linux / Python 3.7 wheel for pySBOL-2.3.2? If I can get a wheel for this I'm happy to test. I wonder if there isn't some appropriate abstraction layer that can tell you where to look, that could be used instead of this workaround in the future? As I remember I did not have any SSL issues when I built the Python bindings from libSBOL directly.

[bbartley]

@tim-tx There is now a Python 3.7 wheel available for Linux that should auto-configure the certificate path. It seems to work on Ubuntu and CentOS so far:

pip3 install pysbol --upgrade --user

You should get:
Successfully installed pysbol-2.3.3.post6