Add a prototype of Sample::developmental_stage backfill script

[arkid15r]

Issue Number

#3438

Purpose/Implementation Notes

This is a draft/prototype of a Foreman command to use for Sample::developmental_stage backfill process. The code is untested and supports SRA source DB only.

Types of changes

What types of changes does your code introduce?

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

Checklist

• Lint and unit tests pass locally with my changes
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if appropriate)
• Any dependent changes have been merged and published in downstream modules

[davidsmejia]

Looking good, a couple comments about approach.

Looking forward, I think that we will want to update the _apply_harmonized_metadata_to_sample to specifically handle updates vs new samples. This depends on what the science team says is appropriate.

[davidsmejia]

• We will probably want last_refreshed on Experiment as well, since a sample could belong to more than one experiment.
• We probably want to add last_refresh_failure as a timestamp on both as well to help with re-running

[davidsmejia]

This takes sample as the first argument

[davidsmejia]

One more consideration here is that after updating the sample we will want to update the cached values on experiment.

ie:

refinebio/foreman/data_refinery_foreman/surveyor/external_source.py

Lines 207 to 211 in 07d3759

	# Update our cached values
	experiment.update_num_samples()
	experiment.update_sample_metadata_fields()
	experiment.update_platform_names()
	experiment.save()