SSL verfication failure contacting toolshed site

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I have installed Galaxy on SUSE Linux Enerprise v15.1. If I go to the admin page and select “Install and Uninstall” under the Tool Management section of the menu on the left-hand side I get the following error:

Invalid server response. HTTPSConnectionPool(host=‘toolshed.g2.bx.psu.edu’, port=443): Max retries exceeded with url: /api/categories (Caused by SSLError(SSLError(1, ‘[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)’),)).

I have been unable to determine if the certificate that is not being verified is from the toolshed site or if the toolshed site is not verifying out certificate. Strangely enough we can successfully display the toolshed site in a browser on the VM. Other tests with curl and python have been able to connect to the site without error.

The script inside Galaxy that seems to generate the error is in scripts/tool_shed/api/create_categories.py.

Is there some configuration required in order to connect to external tool shed sites?

Any help on debugging this problem would be appreciated.

Thanks in advance.

1 Like
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HI @pdagosto

The admin docs for the function are here: Tool Shed API Documentation — Galaxy Project 23.1.1.dev0 documentation

Generating and including an API key is the first step. Has that been done?

Let’s start there :slight_smile:

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Yes, I have an API key

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@pdagosto

I’m not sure what else to check next, so let’s ask the admins for more advice at Gitter. They may reply here or there, and feel free to join the chat. galaxyproject/admins - Gitter

Update: Actually, there is one more piece of info that would help … what version of Galaxy did you install? The 21.09 release is not quite ready yet, so the latest stable version is still 21.05: Releases — Galaxy Project 21.05.1.dev0 documentation. Is that what you are using? Any others could be problematic.

Prior Q&A Ref: Search results for 'ssl' - Galaxy Community Help

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The version I was asked to install is 21.01.

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Thanks – the admin feedback is this:

python env seems to be missing certs

installing certifi would solve the problem but should be part of the default install (is a Galaxy requirement)

Maybe check the logs from when you started up Galaxy the first time to see if that dependency didn’t install correctly for some reason?

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It seems to be there in the Galaxy virtual environment:

(.venv) [ ~]$ pip show certifi
Name: certifi
Version: 2020.12.5
Summary: Python package for providing Mozilla's CA Bundle.
Home-page: https://certifiio.readthedocs.io/en/latest/
Author: Kenneth Reitz
Author-email: me@kennethreitz.com
License: MPL-2.0
Location: /opt/galaxy/.venv/lib/python3.6/site-packages
Requires:
Required-by: requests, bdbag
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It seems to be there in the Galaxy virtual environment. I tried to post the console output (using the code tag) but I can’t see my many tries at sending my reply in the thread.