Update packages to fix vulnerabilities

[khaledk2]

This PR updates packages to address known vulnerabilities in dependency packages, i.e.
https://github.com/ome/omero_search_engine/security/dependabot

I believe it’s important to include these changes in the next tag and release.
It has been deployed on the ide-testing

cc @pwalczysko @jburel

[jburel]

Apart from urllib3 the other packages are point releases.
This will need to be tested before we do anything

[khaledk2]

Understood.
I’ve carried out some initial testing and haven’t encountered any issues so far.
I’ll complete further checks to confirm we’re good to proceed.

[pwalczysko]

@khaledk2 Do you have the docker image similarly to #127 and ome/ansible-role-omero-searchengine#16 (comment) ? If yes, I could start testing using the ansible role.

[khaledk2]

@khaledk2 Do you have the docker image similarly to #127 and ome/ansible-role-omero-searchengine#16 (comment) ? If yes, I could start testing using the ansible role.

@pwalczysko, I have updated the Docker image khaledk2/searchengine:lat to include this PR.

You should run the following command to use the updated Docker image

docker pull khaledk2/searchengine:lat

[khaledk2]

I have carried out the following tests on idr-testing:

• Deleting a container (idr0173-breiter-alphasynuclein/experimentA), indexing it again, and then building the cache using these commands.

  • sudo docker run -v /data/searchengine/searchengine/:/etc/searchengine/ -v /data/searchengine/searchengine/logs/:/opt/app-root/src/logs/ --network searchengine-net khaledk2/searchengine:lat delete_containers -i 3203 -r project -u true -s idr

  • sudo docker run -v /data/searchengine/searchengine/:/etc/searchengine/ -v /data/searchengine/searchengine/logs/:/opt/app-root/src/logs/ --network searchengine-net khaledk2/searchengine:lat index_container_from_database -i 3203 -d idr -r project

  • sudo docker run -v /data/searchengine/searchengine/:/etc/searchengine/ -v /data/searchengine/searchengine/logs/:/opt/app-root/src/logs/ --network searchengine-net khaledk2/searchengine:lat update_data_source_cache -d idr

• Generates the containers' BBF files.

• In addition, I’ve tested both the asynchronous queries and the standard ones.

All the tests passed, and everything worked as expected.

[pwalczysko]

Tested via the ansible-role-omero-searchengine on RHEL 9 VM. Used the docker pull... cmd as per #140 (comment).

The basic tests as per https://github.com/ome/ansible-role-omero-searchengine?tab=readme-ov-file#idr-searcher are passing