[POST-berkeley-MERGER] Update FunctionalAnnotationAggMember class for compatibility with MetaP Aggregation tables
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kheal
changed the title
FunctionalAnnotationAggMember class for compatibility with MetaP Aggregation tables
kheal
changed the title
FunctionalAnnotationAggMember class for compatibility with MetaP Aggregation tablesberkeley-MERGER] Update FunctionalAnnotationAggMember class for compatibility with MetaP Aggregation tables
src/schema/nmdc.yaml
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| structured_pattern: | ||
| syntax: "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}$" | ||
| syntax: "{id_nmdc_prefix}:(wfmgan|wfmp)-{id_shoulder}-{id_blade}{id_version}$" |
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backmerge such that mfmtan is also a valid typecode.
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@aclum - you mean "wfmtan", correct? MetatranscriptomeAnnotation class?
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can someone remind me the decision on when we'd start using a deprecated.yaml file? @sierra-moxon this pr deprecates quite a bit so it would be nice use. |
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@aclum we decided not to start forcing the use until after berkeley roll out, but there's no reason you can't still put the pieces in the deprecated.yaml. |
| @@ -255,16 +255,23 @@ classes: | |||
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| FunctionalAnnotationAggMember: | |||
| class_uri: nmdc:FunctionalAnnotationAggMember | |||
| unique_keys: | |||
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leaving a note here to make sure @turbomam or @sierra-moxon review this use of unique_keys (in response to microbiomedata#2155)
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Have we discussed this at all? @kheal do you still want to discuss the use of unique_keys even though the PR is closed?
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I have moved this PR to the nmdc-schema repo: microbiomedata#2203. I'd appreciate input on the unique_keys use there.
Description
This PR will
FunctionalAnnotationAggMemberclass to be able to accomodate both annotations from metagenomics and metaproteomics analyses. This is accomplished by exchanging the slotmetagenome_anlaysis_idwith the existing slotwas_generated_by.metagenome_anlaysis_idslot as there are now no classes using this slot.countslotFunctionalAnnotationAggMemberclass that is a combination ofwas_generated_byandgene_function_idThis PR will close 1253 and 2155 and partially address 2028
Reviewers
For review (when out of draft stage):
@mslarae13, @aclum, @SamuelPurvine, @eecavanna
To keep informed:
@naglepuff, @mbthornton-lbl, @corilo, @sujaypatil96, @brynnz22
PR Information
What type of PR is this? (check all applicable)
slotRelated Issues
Did you add/update any tests?
Could this schema change make it so any valid data becomes invalid?
If you answered "Yes", does this PR branch include that migrator?
Does this PR have any downstream implications?
We will need to update the aggregation scripts (issue filed here: Update generate_metap_agg.py script to source ids from new slot nmdc-aggregator#13) and the data portal to use the new slot