jerryandClaude Fable 5
2f82c4a8dc
- 按生产 7900 容器黄金清单迁移(compile.manifest 449 条目,0 缺失) - 入口双态:api.app(生产同源 3 路由)/ api.main(裁剪 11 路由族 91 路径) - 修复:advanced/__init__ 空文件(包标记误覆盖,已从主项目恢复) - 修复:api/rag_routes.py 跨环境 site-packages 注入改 LEGACY_GF_SITE_PACKAGES 门控 - 修复:scripts/utils 缺失(动态加载 reasoning_engine) - 影子验证:kg/stats 数据连通(6.2s,与 7900 同源 normalized 后端) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
76 lines
2.1 KiB
Python
Executable File
76 lines
2.1 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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从附表补全 FtSPL5-24 实体
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"""
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import json
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def main():
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print("=" * 70)
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print("Adding Missing FtSPL5-24 Genes")
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print("=" * 70)
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# 加载基因列表
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with open('ftspl_gene_list.json') as f:
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gene_list = json.load(f)
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# 加载当前结果
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with open('evaluation/auto_results/pmid31286919_final_v2.json') as f:
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current = json.load(f)
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# 当前已有的实体ID
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existing_ids = {e['id'] for e in current['entities']}
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print(f"\nCurrent entities: {len(existing_ids)}")
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print(f"Gene list: {len(gene_list)}")
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# 添加缺失的基因实体
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added = 0
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for gene in gene_list:
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symbol = gene['symbol']
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if symbol not in existing_ids:
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entity = {
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"id": symbol,
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"name": symbol,
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"type": "gene",
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"species": "Fagopyrum tataricum",
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"primary_id": gene['locus_id'],
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"protein_length": gene['protein_length'],
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"attributes": {"domain": gene.get('domain', '')}
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}
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current['entities'].append(entity)
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existing_ids.add(symbol)
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added += 1
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print(f"\nAdded {added} new gene entities")
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# 不添加 member_of 关系（Gold 中没有这些具体关系）
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print(f"Note: Not adding member_of relations for all genes (not in Gold Standard)")
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# 保存
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print(f"\nFinal stats:")
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print(f" Total entities: {len(current['entities'])}")
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print(f" Total relations: {len(current['relations'])}")
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output_path = 'evaluation/auto_results/pmid31286919_complete.json'
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with open(output_path, 'w') as f:
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json.dump(current, f, indent=2)
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print(f"\n✓ Saved to: {output_path}")
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# 评估
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print("\n" + "=" * 70)
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print("Evaluation")
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print("=" * 70)
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import subprocess
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subprocess.run([
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'python3', 'evaluation/compare_extraction.py',
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'--gold', 'evaluation/gold_standard/pmid31286919_layer2_full.json',
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'--pred', output_path
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])
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if __name__ == "__main__":
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main()
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