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Remove PeptideQuantification class, migrate information from PeptideQuantification best_protein slot to new razor_protein slot on MetaproteomicsAnalysis class #2157

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kheal opened this issue Aug 13, 2024 · 1 comment
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Remove PeptideQuantification class, migrate information from PeptideQuantification best_protein slot to new razor_protein slot on MetaproteomicsAnalysis class #2157

kheal opened this issue Aug 13, 2024 · 1 comment
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kheal commented Aug 13, 2024 •
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This work is proposed to streamline the data in mongo with regards to the MetaproteomicsAnalysis.

See full discussion here: #2152

Resolution from meeting.
We will remove PeptideQuantification class altogether.

We will rename ProteinQuantification class as ProteinIdentification and migrate information from PeptideQuantification class to new slot has_protein_identifications on MetaproteomicsAnalysis class
Screenshot 2024-09-03 at 12 17 57 PM

This will have downstream affects of needing to keep the aggregation script (https://github.com/microbiomedata/nmdc-aggregator/blob/main/generate_metap_agg.py) in step with these metadata changes. Companion issue filed here: microbiomedata/nmdc-aggregator#13

Originally posted by @kheal in #2152 (comment)
@kheal kheal changed the title Remove PeptideQuantification and ProteinQuantification classes, migrate information from PeptideQuantification.best_protein slot to new slot on MetaproteomicsAnalysis class Remove PeptideQuantification and ProteinQuantification classes, migrate information from PeptideQuantification best_protein slot to new slot on MetaproteomicsAnalysis class Aug 13, 2024
This was referenced Aug 13, 2024
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@kheal kheal self-assigned this Aug 20, 2024
@kheal kheal mentioned this issue Aug 21, 2024
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@kheal kheal changed the title Remove PeptideQuantification and ProteinQuantification classes, migrate information from PeptideQuantification best_protein slot to new slot on MetaproteomicsAnalysis class Remove PeptideQuantification class, migrate information from PeptideQuantification best_protein slot to new slot on MetaproteomicsAnalysis class Sep 3, 2024
@kheal kheal changed the title Remove PeptideQuantification class, migrate information from PeptideQuantification best_protein slot to new slot on MetaproteomicsAnalysis class Remove PeptideQuantification class, migrate information from PeptideQuantification best_protein slot to new razor_protein slot on MetaproteomicsAnalysis class Oct 2, 2024
@kheal kheal mentioned this issue Oct 8, 2024
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@kheal kheal linked a pull request Oct 8, 2024 that will close this issue
Refactor MetaproteomicsAnalysis slots and implement migrator #2204
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kheal commented Nov 7, 2024

Closing this issue - see #2250 for path forward

@kheal kheal closed this as not planned Won't fix, can't repro, duplicate, stale Nov 7, 2024
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Refactor MetaproteomicsAnalysis slots and implement migrator microbiomedata/nmdc-schema
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