SSL CA cert error

[dsanleo]

With the last version in linux (2.3.3) I have an error when I try to search in https://synbiohub.org/
For example with the following code extracted from your examples:

igem = PartShop('https://synbiohub.org')
records = igem.search("plasmid")

I have this error

RuntimeError: Attempt to validate online failed with Problem with the SSL CA cert (path? access rights?)

Do you know why it is happening?

[tcmitchell]

Hi @dsanleo,

Depending on the exact version of pySBOL, you may have to upgrade. You may also have to set a config option.

If you're already running pysbol-2.3.3.post6 please post what Linux distribution and version you are running, as well as the specific version of pySBOL.

References:

• SSL issue with pip pysbol package on Linux libSBOL#202 (comment)
• SSL issue with pip pysbol package on Linux libSBOL#202 (comment)

[dsanleo]

Hi @tcmitchell ,
I downloaded the last version, 2.3.3.post7 and I'm running into a Ubuntu 18.04 machine, about the python version I'm using the 3.7.5 version (I checked it with python 3.6 and 2.3.3.post6 too).
I read before the conversations you send me, but I have the same error after using Config.setOption('ca-path','/etc/ssl/certs/ca-certificates.crt')

[tcmitchell]

I can repeat this problem in a fresh Ubuntu 18.04 docker image with pySBOL 2.3.3.post7:

Python 3.6.9 (default, Nov  7 2019, 10:44:02) 
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sbol
>>> sbol.Config.getOption('ca-path')
'/etc/ssl/certs/ca-certificates.crt'
>>> igem = sbol.PartShop('https://synbiohub.org')
>>> records = igem.search('plasmid')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.6/dist-packages/sbol/libsbol.py", line 14683, in search
    return _libsbol.PartShop_search(self, *args)
RuntimeError: Attempt to validate online failed with Problem with the SSL CA cert (path? access rights?)
>>> 

I have confirmed that the root certificate for https://synbiohub.org, "DST Root CA X3", is in /etc/ssl/certs/ca-certificates.crt with a matching fingerprints.

[tcmitchell]

• I think "Attempt to validate online failed" is a red herring. The code in question is not contacting the online validator. This is probably a copy/paste error.
• The C++ code invoked here does not set CURLOPT_CAINFO, which seems the likely culprit in this case. Other PartShop methods do set this option. Perhaps it got missed in this case? Or perhaps there is a reason why it is not set?
• While there, it sure seems like the query string is not being formed correctly, although it does seem to work at SynBioHub.
  • encode_url(search_text); comes after search_text is appended to parameters. Shouldn't it come before?
  • The addition of /?offest= comes after some URL parameters, like objectType are set. That feels wrong, but it does seem to work when typed manually at https://synbiohub.org

@bbartley do you have thoughts? Or is there a workaround for @dsanleo ?