Refactor MetaproteomicsAnalysis slots and implement migrator
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Add valid and invalid examples for MetaP
eecavanna
approved these changes
Oct 9, 2024
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kheal
changed the title
berkeley-MERGER] Refactor MetaproteomicsAnalysis slots and implement migratorMetaproteomicsAnalysis slots and implement migrator
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This will address #2157.
Full discussion is here for interested parties: #2152.
Overall, this PR will significantly minimize the proteomics data stored as metadata by refactoring the
MetaproteomicsAnalysisclass's contents.This PR
PeptideQuantification,all_proteins,best_protein,min_q_value,peptide_sequence,peptide_sum_masic_abundance,peptide_sequence_count.ProteinQuantificationtoProteinIdentificationto better capture content.MetaproteomicsAnalysisclass -has_protein_identifications. This slot's range will beProteinIdentificationand that class will be populated from thebest_proteinandpeptide_sequence_countslots from the now deprecatedPeptideQuantificationclass.MetaproteomicsAnalysisclass (previously missing), based off of real data currently in Mongo.razor_proteinslot (to address Review id_locus pattern forbest_proteinandall_proteinslots #2028)This PR was moved from microbiomedata#236.
Reviewers
To review: mslarae13, eecavanna, SamuelPurvine
To keep informed: naglepuff, aclum, mbthornton-lbl, corilo, sujaypatil96, brynnz22
PR Information
What type of PR is this? (check all applicable)
classandslotsslotto aclassDescription
See above
Related Issues / Discussions
- Remove
PeptideQuantificationclass, migrate information fromPeptideQuantificationbest_proteinslot to newrazor_proteinslot onMetaproteomicsAnalysisclass #2157 (will be closed after this is merged in)- Review id_locus pattern for
best_proteinandall_proteinslots #2028 (will be closed after this is merged in)- Update generate_metap_agg.py script to source ids from new slot nmdc-aggregator#13 (will be unblocked after this is merged in)
- Proposed actions for de-bloat of metaproteomics data in mongo DB #2152 (discussion of plan for this PR)
Did you add/update any tests?
Added valid and invalid examples as well a doctest for migrator
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?
This work will need to be followed by an update to the aggregator script, an update to the structure of the aggregation tables in the schema and associated migrator, and an update to the DataPortal's handling of the KEGG terms from the aggregations.