TXImport Eligibility - Check if SHORT and LONG indices exist

[davidsmejia]

Issue Number

N/A

Purpose/Implementation Notes

When determining if TXImport can be run on a particular experiment either as part of the Salmon job or run early via the management command run_tximport we verify that the latest trascriptome index is what that salmon job was run with.

The problem encountered prior to this PR is that if the order of transcriptome indices is different, ie SHORT was created after LONG, this function would return SHORT even though we are interested in checking if the latest LONG index matches the index used to process the quant file.

My understanding is that this is to prevent different versions of salmon from being used throughout processing, which this change would still preserve.

This PR makes the following changes:

• Rename get_latest_organism_index to get_latest_organism_indices.
• Renamed method now tries to return a list of the latest short and long index for the organism.
• Additionally, instead of checking equality when confirming the index exists, we now check if the index is contained in the list of the latest for each type.

Methods

n/a or see implementation notes

Types of changes

• Bugfix (non-breaking change which fixes an issue)

Functional tests

tested on staging

Checklist

• [X] Lint and unit tests pass locally with my changes

Screenshots

n/a

[jaclyn-taroni]

Purpose/implementation section seems reasonable 👍🏻 -- I agree with this assessment:

My understanding is that this is to prevent different versions of salmon from being used throughout processing, which this change would still preserve.