complete omics KG build #118
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…rence-backend feat: add inference backends
…robs fix: fix loss_entropy
* feat: add config and operator node types * refactor: refactor readers with ray data * fix: delete param parallelism for readers * fix: fix import error * refactor read and chunk operators with no side effects * fix: fix import error * fix: fix return logic * refactor: rename operator split to chunk * refactor: refactor build_kg to accomodate ray data * feat: add StorageFactory & global params * refactor: refactor quiz to accomodata ray data engine * fix: reload graph before quizzing * Potential fix for pull request finding 'Unreachable code' Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com> * fix: fix quiz params * refactor: refactor quiz&judge to ray actors * fix: fix transferring quizzed data to JudgeService * refactor: refactor partition to accomodate ray data * fix: fix lint problem * refactor: refactor op generate * feat: write results in output folder * fix: raise error when no dataset is created * fix: return generator in ece_partitioner * fix: return generator in ece_partitioner * refactor: refactor data format to support multi-modal input * fix: delete fetching schema to avoid ray's duplicate execution * fix: fix operators' registry * feat: refactor schema_guided_extraction & add examples * feat: seperate ray logs and service logs * feat: use storage actor * feat: add kuzu graph database * feat: add llm as actors * refactor: delete old runner * fix: fix vllm wrapper * docs: update .env.example * fix: use kuzudb in quiz_service * fix: update webui * feat: make storage backend configuragble * docs: update README” --------- Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
… Ray Data architecture with protein QA features
…er (InternScience#117) * fix: fix data type of num_gpus & generate_topk_per_token of vllmwrapper * fix: fix lint error
Summary of ChangesHello @CHERRY-ui8, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed! This pull request delivers a major enhancement by introducing a comprehensive framework for multi-omics knowledge graph construction and question-answer generation. It enables users to process DNA, RNA, and protein data through a unified pipeline, leveraging both online biological databases and efficient local BLAST searches. The changes streamline the workflow for bioinformatics tasks, making it easier to extract structured knowledge and generate relevant QA pairs from complex biological information. Highlights
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Code Review
This is an impressive and substantial pull request that introduces a complete multi-omics knowledge graph generation pipeline. The refactoring of the search operators, configuration management, and asynchronous handling is excellent and greatly improves the robustness and user experience of the codebase. The new features are well-documented in the added README file. I have a few suggestions to further enhance correctness and maintainability.
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…ne ID access in NCBISearch
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…sted formatting in `base_operator.py`, `base_searcher.py`, and `anchor_bfs_partitioner.py` for consistency. Removed unnecessary blank lines in `json_reader.py`, `rnacentral_searcher.py`, and other template files to improve readability.
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