add: search multi omics#140

Merged

ChenZiHong-Gavin merged 25 commits intoInternScience:mainfrom

CHERRY-ui8:search-multi-omics

Dec 25, 2025

Commits on Dec 24, 2025

Commits on Dec 25, 2025

refactor: update multi-omcis eg. input to use specific data types
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refactor: update input format in README files and base_reader
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chore: add kv_backend and graph_backend params to search config files
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refactor: implement lazy imports in BaseOperator to avoid circular dependencies
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refactor: remove unnecessary asyncio locks and thread pool in searchers
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refactor: update SearchService to use specific search classes, implement async search wrapper and remove unnecessary search output keys
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style: fix pylint problems
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fix: change async BaseSearcher to sync to match DNA, RNA and protein searchers
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fix: pass threshold in searcher config
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fix: delete duplicate logger
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Merge branch 'main' of https://github.com/open-sciencelab/GraphGen into search-multi-omics
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perf: perf search service
ChenZiHong-Gavin
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Merge branch 'main' of https://github.com/open-sciencelab/GraphGen into search-multi-omics

ChenZiHong-Gavin
authored and
CHERRY-ui8
committed
fix: fix pylint problems (extract sequence parsing and local search logic of RNA and prot search)
CHERRY-ui8
committed