kbase / execution_engine2

KBase Execution Engine

http://www.kbase.us/services/ee2

MIT License

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SECURITY-36 3.10.10 #477

Closed bio-boris closed 3 months ago

bio-boris commented 4 months ago

Description of PR purpose/changes

Update clients to work with mongo7 by updating pymongo and mongoengine
Fix linting issues from flake8 and black
Update outdated libraries that can no longer be pip installed
The latest Dockerfile build contains conda which installs python 3.12.4 so these changes will pin python to 3.10 and save us headache in the future
Speed up tests by moving docker build step out
Create matrix of tests to run against mongo3.6 and mongo7

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 88.68%. Comparing base (1307bce) to head (db1acc5). Report is 303 commits behind head on develop.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #477 +/- ## =========================================== + Coverage 83.84% 88.68% +4.84% =========================================== Files 22 29 +7 Lines 1993 2740 +747 =========================================== + Hits 1671 2430 +759 + Misses 322 310 -12 ```

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Xiangs18 commented 3 months ago

@bio-boris Both Kafka and ZooKeeper containers exit after starting them with Docker Compose. Is this expected?

bio-boris commented 3 months ago

@Xiangs18 Kafka seems to stay up when I try it, but zookeeper crashes. It looks like the tests still pass (But throw warnings in the logs when they are removed the docker-compose file as per https://github.com/kbase/execution_engine2/pull/485/ )

Xiangs18 commented 3 months ago

bio-boris commented 3 months ago

We discussed this oob

We deployed this to CI
Ran a job
Checked job logs
Checked the job browser

And things are working