survey transcriptome index strain mapping on assembly

[davidsmejia]

Issue Number

3381

Purpose/Implementation Notes

• took logic that fetches and searches results into a static method on transcriptome index surveyor
• change logic when surveying fungi/bacteria from checking name to checking assembly
• override the species_taxonomy_id for bacteria and fungi
• throw an error if more than one assembly matches when surveying transcriptome (requires manual intervention)
• merge and extend tests to check if surveyed files exist remotely
• fix issue for bacteria download files where assembly has an underscore after in file name
• recreate the cached requests cassettes

Methods

In order to create the correct Bacteria and Fungi this PR contains a change that requires us to include the species_taxonom_id in config/organism_strain_mapping.csv. This value should be the NCBI taxonomy ID of the organism that we want the strain to represent. This value comes back matching for bacteria so we must specify it now or we will create strain organisms when creating / saving to the DB.

Types of changes

• New feature (non-breaking change which adds functionality)
• Bug Fix

Functional tests

n/a

Checklist

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

Screenshots

n/a

[davidsmejia]

Downloader and No-op seem to be failing due to missing ascp / being unable to install. I think this is good to review at this time.