adminandClaude Fable 5
730692a1f6
- phase2b_converter: result.json -> neo4j.cypher + qdrant_points.jsonl (payload keys replicate direct_flow_retriever contract; kb_version= aqua_srt_v1_20260930_normalized, source_system=Aqua_canonical) - qdrant_loader: bge-m3 embed + batched upsert + checkpoint resume - registry_builder: paper blocks -> registry jsonl (plant format) - batch_runner: manifest -> convert -> neo4j -> qdrant, all checkpointed - start_aqua_kb.sh: user-space trial instances (Neo4j 19889 / Qdrant 27435) - smoke 11/11 green incl. resume drills - aqua configs: entity_alias_aqua.yaml (22 entries), relation_taxonomy_aqua.yaml (45 groups); manifest points to aqua configs - QA artifacts: golden_aqua.jsonl (41 Qs zh/en), qc_standards.md, budget_template.md + cost_model.py (measured pilot tokens) - pilot: 500 MD + 30 PDF extracted, 0 failures; QC stats computed Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
235 lines
12 KiB
Python
235 lines
12 KiB
Python
#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""自造 3 个最小 v16 结构 result.json fixture（手写字段按 v16_1_2 契约）。
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产出 <dir>/<paper_id>/result.json，每篇 3-5 实体 + 3-5 关系，
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含 rejected 关系（验证转换器过滤）与多层 output_layer。
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"""
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from __future__ import annotations
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import json
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from pathlib import Path
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FIXTURES = [
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{
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"paper_id": "doi:10.1016/0044-8486(88)90238-4",
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"paper": {
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"paper_id": "doi:10.1016/0044-8486(88)90238-4",
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"title": "Quality of algal material produced on a fertilizer-tap water medium in outdoor plastic-enclosed systems",
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"doi": "10.1016/0044-8486(88)90238-4",
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"pmid": "",
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"pmcid": "",
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"journal": "Aquaculture",
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"publication_year": "1988",
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},
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"entities": [
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{"name": "Chlorella vulgaris", "type": "species", "name_resolved": "",
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"synonyms": [], "confidence": 0.95},
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{"name": "outdoor plastic-enclosed culture", "type": "culture_system",
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"name_resolved": "", "synonyms": [], "confidence": 0.9},
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{"name": "fertilizer-tap water medium", "type": "culture_medium",
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"name_resolved": "", "synonyms": [], "confidence": 0.9},
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{"name": "protein content", "type": "biochemical_trait",
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"name_resolved": "", "synonyms": [], "confidence": 0.85},
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],
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"relations": [
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{
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"source": "Chlorella vulgaris", "source_type": "species",
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"source_resolved": "Chlorella vulgaris", "source_type_resolved": "species",
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"relation": "cultured_in", "relationship_resolved": "cultured_in",
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"target": "outdoor plastic-enclosed culture", "target_type": "culture_system",
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"target_resolved": "outdoor plastic-enclosed culture",
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"target_type_resolved": "culture_system",
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"relation_category": "cultivation",
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"evidence": "C. vulgaris was maintained in outdoor plastic-enclosed systems with fertilizer-tap water medium.",
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"confidence": 0.95, "output_layer": "main_kg", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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{
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"source": "Chlorella vulgaris", "source_type": "species",
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"source_resolved": "Chlorella vulgaris", "source_type_resolved": "species",
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"relation": "cultured_in", "relationship_resolved": "cultured_in",
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"target": "fertilizer-tap water medium", "target_type": "culture_medium",
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"target_resolved": "fertilizer-tap water medium",
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"target_type_resolved": "culture_medium",
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"relation_category": "cultivation",
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"evidence": "Algal biomass was produced on a fertilizer-tap water medium.",
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"confidence": 0.9, "output_layer": "main_kg", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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{
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"source": "Chlorella vulgaris", "source_type": "species",
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"source_resolved": "Chlorella vulgaris", "source_type_resolved": "species",
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"relation": "has_trait", "relationship_resolved": "has_trait",
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"target": "protein content", "target_type": "biochemical_trait",
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"target_resolved": "protein content", "target_type_resolved": "biochemical_trait",
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"relation_category": "physiological_measurement",
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"evidence": "Protein content of the harvested biomass reached 45% of dry weight.",
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"confidence": 0.85, "output_layer": "main_kg", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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{
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"source": "Chlorella vulgaris", "source_type": "species",
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"source_resolved": "Chlorella vulgaris", "source_type_resolved": "species",
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"relation": "grows_in", "relationship_resolved": "grows_in",
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"target": "fertilizer-tap water medium", "target_type": "culture_medium",
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"target_resolved": "fertilizer-tap water medium",
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"target_type_resolved": "culture_medium",
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"relation_category": "growth_condition",
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"evidence": "Growth rates were stable across seasons.",
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"confidence": 0.6, "output_layer": "rejected", "claim_scope": "",
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"candidate_status": "rejected", "triple_quality": "", "final_action": "",
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},
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],
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"chunks": [], "sections": [],
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"metadata": {"version": "16.1.2"},
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},
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{
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"paper_id": "doi:10.2331/suisan.54.1049",
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"paper": {
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"paper_id": "doi:10.2331/suisan.54.1049",
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"title": "Titration of the alternative complement pathway activity of representative cultured fishes",
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"doi": "10.2331/suisan.54.1049",
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"pmid": "", "pmcid": "", "journal": "Nippon Suisan Gakkaishi",
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"publication_year": "1988",
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},
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"entities": [
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{"name": "Oncorhynchus mykiss", "type": "species", "name_resolved": "",
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"synonyms": [], "confidence": 0.95},
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{"name": "alternative complement pathway", "type": "immune_pathway",
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"name_resolved": "", "synonyms": [], "confidence": 0.9},
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{"name": "serum", "type": "biological_sample", "name_resolved": "",
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"synonyms": [], "confidence": 0.9},
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],
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"relations": [
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{
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"source": "Oncorhynchus mykiss", "source_type": "species",
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"source_resolved": "Oncorhynchus mykiss", "source_type_resolved": "species",
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"relation": "activates", "relationship_resolved": "activates",
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"target": "alternative complement pathway", "target_type": "immune_pathway",
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"target_resolved": "alternative complement pathway",
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"target_type_resolved": "immune_pathway",
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"relation_category": "immune_function",
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"evidence": "Serum from rainbow trout showed ACH50 activity of 142 U/ml.",
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"confidence": 0.95, "output_layer": "main_kg", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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{
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"source": "alternative complement pathway", "source_type": "immune_pathway",
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"source_resolved": "alternative complement pathway",
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"source_type_resolved": "immune_pathway",
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"relation": "measured_in", "relationship_resolved": "measured_in",
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"target": "serum", "target_type": "biological_sample",
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"target_resolved": "serum", "target_type_resolved": "biological_sample",
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"relation_category": "physiological_measurement",
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"evidence": "The ACP titer was titrated in serum samples.",
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"confidence": 0.9, "output_layer": "main_kg", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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{
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"source": "Oncorhynchus mykiss", "source_type": "species",
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"source_resolved": "Oncorhynchus mykiss", "source_type_resolved": "species",
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"relation": "has_sample", "relationship_resolved": "has_sample",
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"target": "serum", "target_type": "biological_sample",
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"target_resolved": "serum", "target_type_resolved": "biological_sample",
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"relation_category": "experimental_material",
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"evidence": "Blood was collected from the caudal vein.",
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"confidence": 0.8, "output_layer": "background_relations", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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],
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"chunks": [], "sections": [],
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"metadata": {"version": "16.1.2"},
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},
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{
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"paper_id": "doi:10.1051/alr/1989009",
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"paper": {
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"paper_id": "doi:10.1051/alr/1989009",
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"title": "Suitability of brackish water tilapia species from the Ivory Coast for lagoon aquaculture. I - Reproduction",
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"doi": "10.1051/alr/1989009",
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"pmid": "", "pmcid": "", "journal": "Aquatic Living Resources",
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"publication_year": "1989",
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},
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"entities": [
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{"name": "Oreochromis niloticus", "type": "species", "name_resolved": "",
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"synonyms": [], "confidence": 0.95},
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{"name": "lagoon aquaculture", "type": "culture_system",
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"name_resolved": "", "synonyms": [], "confidence": 0.9},
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{"name": "Ivory Coast", "type": "location", "name_resolved": "",
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"synonyms": [], "confidence": 0.9},
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{"name": "reproductive performance", "type": "biological_trait",
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"name_resolved": "", "synonyms": [], "confidence": 0.85},
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],
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"relations": [
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{
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"source": "Oreochromis niloticus", "source_type": "species",
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"source_resolved": "Oreochromis niloticus", "source_type_resolved": "species",
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"relation": "suited_for", "relationship_resolved": "suited_for",
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"target": "lagoon aquaculture", "target_type": "culture_system",
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"target_resolved": "lagoon aquaculture",
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"target_type_resolved": "culture_system",
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"relation_category": "aquaculture_suitability",
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"evidence": "O. niloticus showed the best reproduction performance among brackish water tilapias.",
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"confidence": 0.9, "output_layer": "main_kg", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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{
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"source": "Oreochromis niloticus", "source_type": "species",
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"source_resolved": "Oreochromis niloticus", "source_type_resolved": "species",
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"relation": "native_to", "relationship_resolved": "native_to",
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"target": "Ivory Coast", "target_type": "location",
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"target_resolved": "Ivory Coast", "target_type_resolved": "location",
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"relation_category": "geographic_distribution",
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"evidence": "Tilapia populations were sampled in lagoons of the Ivory Coast.",
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"confidence": 0.85, "output_layer": "main_kg", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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{
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"source": "Oreochromis niloticus", "source_type": "species",
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"source_resolved": "Oreochromis niloticus", "source_type_resolved": "species",
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"relation": "has_trait", "relationship_resolved": "has_trait",
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"target": "reproductive performance", "target_type": "biological_trait",
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"target_resolved": "reproductive performance",
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"target_type_resolved": "biological_trait",
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"relation_category": "reproductive_biology",
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"evidence": "Mean fecundity was 1200 eggs per female.",
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"confidence": 0.8, "output_layer": "main_kg", "claim_scope": "paper",
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"candidate_status": "", "triple_quality": "", "final_action": "",
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},
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],
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"chunks": [], "sections": [],
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"metadata": {"version": "16.1.2"},
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},
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]
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def main() -> None:
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import argparse
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parser = argparse.ArgumentParser()
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parser.add_argument("--out", default="fixtures")
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args = parser.parse_args()
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root = Path(args.out)
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for fixture in FIXTURES:
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paper_dir = root / fixture["paper_id"].replace("/", "_")
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paper_dir.mkdir(parents=True, exist_ok=True)
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(paper_dir / "result.json").write_text(
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json.dumps(fixture, ensure_ascii=False, indent=2), encoding="utf-8"
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)
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print(f"wrote {paper_dir}/result.json")
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# pilot manifest
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manifest = {
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"papers": [
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{"paper_id": paper["paper_id"], "result": f"{paper['paper_id'].replace(chr(47), chr(95))}/result.json",
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"paper": paper["paper"]}
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for paper in FIXTURES
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]
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}
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(root / "pilot_manifest.json").write_text(
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json.dumps(manifest, ensure_ascii=False, indent=2), encoding="utf-8"
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)
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print(f"wrote {root}/pilot_manifest.json")
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if __name__ == "__main__":
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main()
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