Delete sequence files from file system via cleanup script

[ksierks]

Description of changes

Created a script to delete sequence files from local file system that have already been previously deleted from the database.
Previously deleted sequence files are retrieved from the audit table, because of the inconsistent way they are removed within IRIDA.
The intention is for this script to be run once to do an initial cleanup the file system. There will be subsequent PRs addressing ongoing file clean up.

Steps to test

• create a new sequence run via the irida_uploader
• login to IRIDA as admin and delete the newly created sequence run
• run the purge_sequence_files script.py

Related issue

#1125

Checklist

Things for the developer to confirm they've done before the PR should be accepted:

• CHANGELOG.md (and UPGRADING.md if necessary) updated with information for new change.
• [ ] Tests added (or description of how to test) for any new features.
• [ ] User documentation updated for UI or technical changes.

[deepsidhu85]

@ksierks Hi Katherine, I see that the script cleans up files on the local file storage system but not from cloud storage (aws, azure). Are you planning on adding that in here or in another PR?

[ksierks]

@ksierks Hi Katherine, I see that the script cleans up files on the local file storage system but not from cloud storage (aws, azure). Are you planning on adding that in here or in another PR?

Hi Deep. I wasn't planning on it, unless told otherwise. The file system has 10+ years worth of files. IRIDA hasn't been installed in the cloud that I know of. The intention is to only run the script once and have IRIDA cleanup files.

[deepsidhu85]

@ksierks Hi Katherine, I see that the script cleans up files on the local file storage system but not from cloud storage (aws, azure). Are you planning on adding that in here or in another PR?

Hi Deep. I wasn't planning on it, unless told otherwise. The file system has 10+ years worth of files. IRIDA hasn't been installed in the cloud that I know of. The intention is to only run the script once and have IRIDA cleanup files.

Sorry about that Katherine. I missed the part in the description where the ongoing cleanup will be addressed in subsequent prs. Disregard my above comment! :)

[deepsidhu85]

Looks good to me!

[JeffreyThiessen]

Looks good. Just a few small changes.

[JeffreyThiessen]

Looks good