diff --git a/agent/legacy-rag/compile.exclude-v13-v15 b/agent/legacy-rag/compile.exclude-v13-v15 new file mode 100644 index 0000000..aa76e2c --- /dev/null +++ b/agent/legacy-rag/compile.exclude-v13-v15 @@ -0,0 +1,182 @@ +src/rag/extractors/v13/pc_data_loader +src/rag/extractors/v13/pc_pattern_importer +src/rag/extractors/v13/phase1_document_parser +src/rag/extractors/v13/phase1_document_parser_mineru +src/rag/extractors/v13/phase2_supplementary +src/rag/extractors/v13/phase3_entity_recognition +src/rag/extractors/v13/phase4_relation_extraction +src/rag/extractors/v13/phase5_post_processing +src/rag/extractors/v13/phase5_review +src/rag/extractors/v13/phase6_5_figure_caption +src/rag/extractors/v13/phase6_vlm_image_extraction +src/rag/extractors/v13/v13_extractor +src/rag/extractors/v14/entity_linker +src/rag/extractors/v14/llm_definition_generator +src/rag/extractors/v14/neo4j_store_v14 +src/rag/extractors/v14/pc_data_loader +src/rag/extractors/v14/pc_pattern_importer +src/rag/extractors/v14/pc_patterns_loader +src/rag/extractors/v14/phase1_document_parser +src/rag/extractors/v14/phase1_document_parser_mineru +src/rag/extractors/v14/phase2_supplementary +src/rag/extractors/v14/phase3_entity_recognition +src/rag/extractors/v14/phase4_relation_extraction +src/rag/extractors/v14/phase5_post_processing +src/rag/extractors/v14/phase5_review +src/rag/extractors/v14/phase6_5_figure_caption +src/rag/extractors/v14/phase6_vlm_image_extraction +src/rag/extractors/v14/self_learning +src/rag/extractors/v14/v14_extractor +src/rag/extractors/v14/v14_logger +src/rag/extractors/v15/chunk_builder +src/rag/extractors/v15/chunk_builder_v15_2_1 +src/rag/extractors/v15/chunk_builder_v15_2_2 +src/rag/extractors/v15/chunk_builder_v15_2_3 +src/rag/extractors/v15/chunk_builder_v15_2_4 +src/rag/extractors/v15/chunk_builder_v15_2_5 +src/rag/extractors/v15/entity_linker +src/rag/extractors/v15/llm_definition_generator +src/rag/extractors/v15/methodology_reviewer +src/rag/extractors/v15/neo4j_store_v15 +src/rag/extractors/v15/pc_data_loader +src/rag/extractors/v15/pc_pattern_importer +src/rag/extractors/v15/pc_patterns_loader +src/rag/extractors/v15/phase1_document_parser +src/rag/extractors/v15/phase1_document_parser_mineru +src/rag/extractors/v15/phase2_supplementary +src/rag/extractors/v15/phase3_entity_recognition +src/rag/extractors/v15/phase4_5_triple_canonicalization +src/rag/extractors/v15/phase4_6_relation_semantic_review +src/rag/extractors/v15/phase4_llm_relation_extraction +src/rag/extractors/v15/phase4_llm_relation_extraction_v15_2_1 +src/rag/extractors/v15/phase4_relation_extraction +src/rag/extractors/v15/phase5_post_processing +src/rag/extractors/v15/phase5_review +src/rag/extractors/v15/phase6_5_figure_caption +src/rag/extractors/v15/phase6_vlm_image_extraction +src/rag/extractors/v15/relation_block_builder +src/rag/extractors/v15/self_learning +src/rag/extractors/v15/v15_extractor +src/rag/extractors/v15/v15_logger 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+src/rag/extractors/v15_3_4/phase5_review +src/rag/extractors/v15_3_4/phase6_5_figure_caption +src/rag/extractors/v15_3_4/phase6_vlm_image_extraction +src/rag/extractors/v15_3_4/relation_block_builder +src/rag/extractors/v15_3_4/self_learning +src/rag/extractors/v15_3_4/v15_extractor +src/rag/extractors/v15_3_4/v15_logger diff --git a/agent/legacy-rag/compile.manifest b/agent/legacy-rag/compile.manifest index 9a4d501..e87a921 100644 --- a/agent/legacy-rag/compile.manifest +++ b/agent/legacy-rag/compile.manifest @@ -105,188 +105,6 @@ src/rag/extractors/smart_gene_family_extractor src/rag/extractors/smart_gene_family_extractor_v2 src/rag/extractors/supplementary_downloader src/rag/extractors/unified_data_extractor -src/rag/extractors/v13/pc_data_loader -src/rag/extractors/v13/pc_pattern_importer -src/rag/extractors/v13/phase1_document_parser -src/rag/extractors/v13/phase1_document_parser_mineru -src/rag/extractors/v13/phase2_supplementary -src/rag/extractors/v13/phase3_entity_recognition 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+src/rag/extractors/v16_1_2/chunk_builder_v15_2_3 +src/rag/extractors/v16_1_2/chunk_builder_v15_2_4 +src/rag/extractors/v16_1_2/chunk_builder_v15_2_5 +src/rag/extractors/v16_1_2/entity_linker +src/rag/extractors/v16_1_2/entity_validator_v16_1_1 +src/rag/extractors/v16_1_2/llm_definition_generator +src/rag/extractors/v16_1_2/methodology_reviewer +src/rag/extractors/v16_1_2/neo4j_store_v15 +src/rag/extractors/v16_1_2/paper_metadata_enricher_v16_1_2 +src/rag/extractors/v16_1_2/pc_data_loader +src/rag/extractors/v16_1_2/pc_pattern_importer +src/rag/extractors/v16_1_2/pc_patterns_loader +src/rag/extractors/v16_1_2/phase1_5_mineru_block_builder +src/rag/extractors/v16_1_2/phase1_document_parser +src/rag/extractors/v16_1_2/phase1_document_parser_mineru +src/rag/extractors/v16_1_2/phase2_supplementary +src/rag/extractors/v16_1_2/phase3_entity_recognition +src/rag/extractors/v16_1_2/phase4_5_soft_gate_v16_1_1 +src/rag/extractors/v16_1_2/phase4_5_triple_canonicalization +src/rag/extractors/v16_1_2/phase4_6_layer_assignment_v16_1_1 +src/rag/extractors/v16_1_2/phase4_6_relation_semantic_review +src/rag/extractors/v16_1_2/phase4_llm_relation_extraction +src/rag/extractors/v16_1_2/phase4_llm_relation_extraction_v15_2_1 +src/rag/extractors/v16_1_2/phase4_llm_srt_extraction_v16_1_1 +src/rag/extractors/v16_1_2/phase4_llm_srt_extraction_v16_1_2 +src/rag/extractors/v16_1_2/phase4_relation_extraction +src/rag/extractors/v16_1_2/phase5_post_processing +src/rag/extractors/v16_1_2/phase5_review +src/rag/extractors/v16_1_2/phase6_5_figure_caption +src/rag/extractors/v16_1_2/phase6_vlm_image_extraction +src/rag/extractors/v16_1_2/relation_block_builder +src/rag/extractors/v16_1_2/relation_unit_builder_v16_1_1 +src/rag/extractors/v16_1_2/relation_unit_builder_v16_1_2 +src/rag/extractors/v16_1_2/sectionizer_v16_1_1 +src/rag/extractors/v16_1_2/sectionizer_v16_1_2 +src/rag/extractors/v16_1_2/self_learning +src/rag/extractors/v16_1_2/v15_extractor +src/rag/extractors/v16_1_2/v15_logger +src/rag/extractors/v16_1_2/v16_extractor +src/rag/family_facts +src/rag/hybrid_retriever +src/rag/hybrid_retriever_fixed +src/rag/kg_builder +src/rag/kg_rag_fusion +src/rag/literature_monitor +src/rag/metadata_extractor +src/rag/multi_hop_rag +src/rag/multimodal +src/rag/pc_compatibility_mapper +src/rag/pdf_extractor +src/rag/project_config +src/rag/qa_v1_0_0/answer_composer +src/rag/qa_v1_0_0/api +src/rag/qa_v1_0_0/audit +src/rag/qa_v1_0_0/claim_verifier +src/rag/qa_v1_0_0/config +src/rag/qa_v1_0_0/domain_config +src/rag/qa_v1_0_0/entity_validation +src/rag/qa_v1_0_0/evidence_assessor +src/rag/qa_v1_0_0/evidence_filter +src/rag/qa_v1_0_0/evidence_pack +src/rag/qa_v1_0_0/fusion +src/rag/qa_v1_0_0/hypothesis_extractor +src/rag/qa_v1_0_0/llm_client +src/rag/qa_v1_0_0/pc_retriever +src/rag/qa_v1_0_0/pipeline +src/rag/qa_v1_0_0/provisional_answer +src/rag/qa_v1_0_0/query_builder +src/rag/qa_v1_0_0/reranker +src/rag/qa_v1_0_0/retrieval +src/rag/qa_v1_0_0/schemas +src/rag/qa_v1_0_0/v16_retriever +src/rag/query_rewriter +src/rag/reranker +src/rag/retriever +src/rag/temporal/kg_builder_with_time +src/rag/temporal/neo4j_store +src/rag/temporal/paper_time_extractor +src/rag/temporal/pubmed_time_extractor +src/rag/temporal/temporal_entity +src/rag/temporal/temporal_graph +src/rag/temporal/temporal_query +src/rag/temporal/temporal_relation +src/rag/temporal/time_extractor +src/rag/unified/bbav5_capability +src/rag/unified/bbav5_job +src/rag/unified/bbav5_methodology_config +src/rag/unified/case_package +src/rag/unified/case_qa +src/rag/unified_converter +src/rag/unified/evidence_sentence_boundary +src/rag/unified/figure_table_planner +src/rag/unified/llm_methodology_extractor +src/rag/unified/llm_provider +src/rag/unified/methodology +src/rag/unified/methodology_extractor +src/rag/unified/methodology_payload_validator +src/rag/unified/methodology_qa_sandbox +src/rag/unified/methodology_reviewer +src/rag/unified/parsed_document +src/rag/unified/pipeline +src/rag/unified/rnaseq_source +src/rag/unified/schema +src/rag/unified/simulated_data +src/rag/unified/stage_aware_methodology +src/rag/utils/accession_regex +src/rag/v15_agentic_planner +src/rag/v15_agentic_qa_routes +src/rag/v15_hybrid_retriever +src/rag/vector_store +src/rag/vector_store_qdrant +src/rag/web_search +src/schemas/manifest +src/utils/accession_regex +tools/audit_functional_surface_parity +tools/audit_migration_requirements +tools/audit_open_source_readiness +tools/runtime_surface +tools/validate_v16_baseline diff --git a/agent/legacy-rag/compile.whitelist b/agent/legacy-rag/compile.whitelist index 4aa73b0..f219e66 100644 --- a/agent/legacy-rag/compile.whitelist +++ b/agent/legacy-rag/compile.whitelist @@ -4,7 +4,8 @@ src/rag/cache/redis_cache.py # 源码 bug:裸变量 prefix(应为 self.prefix),rag-develop 线已修、主项目线未修。 # 该模块 Redis 缓存为死路径(生产未启用 Redis),运行时同样 NameError。 -src/rag/extractors/v15/v15_extractor.py # cython 3.2.4 无法编译(pmid/pdf_path 作用域);主项目线从未在生产编译。 -src/rag/extractors/v15_3_1/v15_extractor.py # 同上(v15_3_1 变体)。 + +# 2026-08-31 瘦身:v15/v15_3_1 两个 bug 模块随 v13-v15 系列整体排除编译 +# (见 compile.exclude-v13-v15;源码保留在仓库,不入编译树) diff --git a/tooling/compile/compile_legacy.sh b/tooling/compile/compile_legacy.sh index 6d7a456..0f8adc2 100755 --- a/tooling/compile/compile_legacy.sh +++ b/tooling/compile/compile_legacy.sh @@ -33,7 +33,7 @@ esac exit 2 } -echo "[legacy 1/6] Copying per compile.manifest ($(wc -l < "$MANIFEST") modules)" +echo "[legacy 1/6] Copying per compile.manifest ($(wc -l < "$MANIFEST") modules; $(wc -l < "$SOURCE_ROOT/compile.exclude-v13-v15" 2>/dev/null || echo 0) excluded v13-v15)" while IFS= read -r rel; do src_file="$SOURCE_ROOT/$rel.py" [[ -f "$src_file" ]] || { echo "MISSING: $rel.py" >&2; exit 3; } @@ -59,9 +59,7 @@ rsync -a "$SOURCE_ROOT/scripts/utils/" "$OUTPUT_DIR/scripts/utils/" 2>/dev/null for d in api scripts src src/db src/llm src/llm/providers src/rag src/rag/advanced \ src/rag/advanced/raptor src/rag/cache src/rag/db src/rag/dual_kb_taxonomy_rag \ src/rag/entity_normalization src/rag/extractors src/rag/extractors/methodology \ - src/rag/extractors/v13 src/rag/extractors/v14 src/rag/extractors/v15 \ - src/rag/extractors/v15_3_1 src/rag/extractors/v15_3_2 src/rag/extractors/v15_3_3 \ - src/rag/extractors/v15_3_4 src/rag/extractors/v16_1_1 src/rag/extractors/v16_1_2 \ + src/rag/extractors/v16_1_1 src/rag/extractors/v16_1_2 \ src/rag/prompts src/rag/qa_v1_0_0 src/rag/temporal src/rag/unified src/rag/utils \ src/schemas src/utils tools; do mkdir -p "$OUTPUT_DIR/$d"