chanzuckerberg / czid-web

Infectious Disease Sequencing Platform

https://czid.org/

MIT License

79 stars 24 forks source link

Update to Python 3 and Ruby 2.5 Buster image #3357

Closed lvreynoso closed 4 years ago

lvreynoso commented 4 years ago

Description

Installs Python 3 on the Docker image for web. The base image is changed to 2.5-buster to make Python 3.7 available.

Python 2 is long out of date and now officially unsupported. However the immediate motivation for this change is for the pipeline visualization work. With the pipeline's workflow described in WDL, parsing the workflow via miniwdl requires Python 3.6+, which 2.5-stretch does not support.

Notes

Part of pipeline visualization work for step function compatibility.

Tests

Server side tests pass, Travis YML updated
No client side code changed

lvreynoso commented 4 years ago

There is one Python script we have: idd2wdl.py for converting dag json files to wdl files. That script is for Python 3 anyways.

I saw the mysql-client package was removed and replaced it with the default-mysql-client, which is a MariaDB client. From my understanding, our version of MySQL is so old that we shouldn't have any issues (and I haven't had any so far).