EVA-3386: Check Ensembl rapid release for supported assemblies #45
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| @@ -29,3 +31,39 @@ def get_supported_asm_from_ensembl(tax_id: int) -> str: | |||
| if assembly_accession_attribute in response: | |||
| return str(response.get(assembly_accession_attribute)) | |||
| return None | |||
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| @lru_cache | |||
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Not sure how this works for cases where the function has no arguments and Python can't compare the input with a previous input... does Python cache the result unconditionally?
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Yes exactly, it's kind of a lazy shorthand for "just call this method once"... I added maxsize=None as I read somewhere it performs a bit better for this use case.
| continue | ||
| current_assembly, current_date = results[tax_id] | ||
| # Keep the more recent assembly, or the lexicographically first one if release dates are equal | ||
| if current_date < release_date or (current_date == release_date and asm_accession < current_assembly): |
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Optional: Guess you have already run an experiment to see if there are cases where release date for an older assembly is more recent than the release date for a newer assembly for some reason (an update/correction to the older assembly perhaps?)
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I've not actually checked this, do you mean comparing against dates in NCBI for example? I'm not sure it's worth doing since this is intended as a short-term measure till Ensembl makes the API public, but we could perhaps ask Ensembl if the scenario you proposed is plausible.
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cc @tcezard As discussed, this does occasionally occur. Here's an example where the later patch has an earlier release date:
And an example where two patch versions have the same release date:
I modified the lexicographical ordering to choose the last rather than the first to account for the second case.
Sundar suggested we could also look at the geneset attribute, but I think at this point it would be preferable to ask Ensembl for clarification and make any necessary changes in a subsequent PR.
| if current_date < release_date or (current_date == release_date and asm_accession < current_assembly): | ||
| results[tax_id] = (asm_accession, release_date) | ||
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| return {key: val[0] for key, val in results.items()} |
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Optional: I am wondering if there is value in storing the release dates somewhere as well for our reference...
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