Add a prototype of Sample::developmental_stage backfill script#3461
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arkid15r wants to merge 1 commit into
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Add a prototype of Sample::developmental_stage backfill script#3461arkid15r wants to merge 1 commit into
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davidsmejia
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Jan 30, 2024
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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.
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| # Auxiliary field for tracking latest metadata update time. | ||
| # Originally added to support Sample::developmental_stage values backfilling. | ||
| last_refreshed = models.DateTimeField(auto_now=True, null=True) |
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- We will probably want
last_refreshedon Experiment as well, since a sample could belong to more than one experiment. - We probably want to add
last_refresh_failureas a timestamp on both as well to help with re-running
| logger.info(f"Refreshing metadata for a sample {sample.accession_code}") | ||
| try: | ||
| _, sample_metadata = SraSurveyor.gather_all_metadata(sample.accession_code) | ||
| SraSurveyor._apply_harmonized_metadata_to_sample(sample_metadata) |
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This takes sample as the first argument
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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
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Issue Number
#3438
Purpose/Implementation Notes
This is a draft/prototype of a Foreman command to use for
Sample::developmental_stagebackfill process. The code is untested and supports SRA source DB only.Types of changes
What types of changes does your code introduce?
Checklist