PlantAI-rag-new/sdk/mock/fixtures/upstream_real_shape_sample.json

{
  "_comment": "真实上游 7920 /api/v1/qa-v1-1-73/search 响应形态样本（DISCOVERY.md §4.1 结构，已截断）——供 normalize 单元测试，不直接作为 API 响应。",
  "success": true,
  "version": "1.1.73",
  "query_id": "20260825_000715_49f801a9",
  "question": "What is the SPL gene family?",
  "answer": "",
  "citation_validation": { "valid": true, "cited_pmids": ["28655295"], "unknown_pmids": [] },
  "sources": [
    {
      "evidence_id": "S1",
      "kb": "V16/V15",
      "source": "SPL gene family",
      "relation": "characterized_in",
      "target": "Oryza sativa",
      "evidence": "## Phylogenetic analysis of the PeSPL genes ...",
      "paper_id": "PMC5488377_12864_2017_Article_3882",
      "title": "Genome-wide analysis of the SPL gene family in pecan",
      "pmid": "28655295",
      "pmcid": "PMC5488377",
      "doi": "10.1186/s12864-017-3882-4",
      "species": "",
      "section": "",
      "output_layer": "main_kg",
      "claim_scope": "",
      "relation_id": "cass_d12f62f9abffbd903b97",
      "retrieval_methods": ["qdrant_vector"],
      "retrieval_queries": ["SPL gene family", "SBP box domain"],
      "vector_score": 0.714,
      "rrf_score": 1.114,
      "rerank_score": 0.989,
      "final_score": 0.982,
      "cluster_id": "clu_0f8da21642adc4f0",
      "cluster_member_count": 3,
      "cluster_member_assertion_ids": ["cass_a", "cass_b", "cass_c"],
      "cluster_member_paper_ids": ["PMC5488377_12864_2017_Article_3882"],
      "cluster_member_pmids": ["28655295"],
      "raw": {
        "kb_version": "V16",
        "source_system": "srt",
        "assertion_id": "cass_d12f62f9abffbd903b97",
        "source": "SPL gene family",
        "relation": "characterized_in",
        "target": "Oryza sativa",
        "evidence": "## Phylogenetic analysis ...",
        "best_evidence": "The SPL gene family is characterized in rice.",
        "paper_id": "PMC5488377_12864_2017_Article_3882",
        "support_count": 12,
        "paper_count": 5,
        "quality_score": 0.91,
        "best_score": 0.95
      }
    }
  ],
  "source_count": 1,
  "evidence_chain_top30": [],
  "provisional_answer": "",
  "retrieval_hypothesis": { "question_type": "raw_question", "direct_question_entities": [], "hypothesized_entities": [], "relation_intents": [], "concept_queries": [], "answer_slots": [], "atomic_claims": [], "negative_constraints": [], "parse_status": "ok" },
  "query_plan": {
    "queries": {},
    "alias_audit": {},
    "agentic_plan": { "anchor_entity": "SPL gene family", "relation_family": "characterized_in" }
  },
  "retrieval_audit": { "qdrant": [], "seed_extraction": {}, "neo4j": [], "dedup": {} },
  "graph_knowledge_chains": {
    "mode": "neo4j_native_path",
    "chain_policy": "display",
    "chains": [
      {
        "chain_id": "G1",
        "chain_source": "neo4j_native_path",
        "hop_count": 2,
        "path_score": 0.861,
        "start": "SPL gene",
        "end": "18 SPL genes in rice",
        "bridge_entities": [],
        "hops": [
          {
            "hop_index": 0,
            "from_id": "cent_spl", "from_name": "SPL gene",
            "to_id": "cent_oryza", "to_name": "Oryza sativa",
            "source": "SPL gene", "relation": "characterized_in", "target": "Oryza sativa",
            "source_type": "gene_family", "target_type": "species",
            "relation_category": "characterized_in",
            "assertion_id": "cass_d12f62f9abffbd903b97",
            "paper_id": "PMC5488377_12864_2017_Article_3882",
            "title": "Genome-wide analysis of the SPL gene family in pecan",
            "pmid": "28655295", "pmcid": "PMC5488377", "doi": "10.1186/s12864-017-3882-4",
            "evidence": "…", "support_count": 12, "paper_count": 5, "best_score": 0.95,
            "edge_score": 0.861
          },
          {
            "hop_index": 1,
            "from_id": "cent_oryza", "from_name": "Oryza sativa",
            "to_id": "cent_18spl", "to_name": "18 SPL genes in rice",
            "source": "Oryza sativa", "relation": "has_gene_family_member", "target": "18 SPL genes in rice",
            "source_type": "species", "target_type": "gene",
            "relation_category": "has_member",
            "assertion_id": "cass_e23a",
            "paper_id": "PMC5488377_12864_2017_Article_3882",
            "title": "Genome-wide analysis of the SPL gene family in pecan",
            "pmid": "28655295", "pmcid": "PMC5488377", "doi": "10.1186/s12864-017-3882-4",
            "support_count": 8, "paper_count": 3, "best_score": 0.88,
            "edge_score": 0.79
          }
        ],
        "score_breakdown": { "path_score": 0.861 }
      }
    ],
    "chain_count": 1,
    "audit": {},
    "summary": { "note": "used_for_answer_generation", "used_for_answer_generation": true }
  },
  "native_graph_chains": [
    {
      "chain_id": "G1",
      "chain_source": "neo4j_native_path",
      "hop_count": 2,
      "path_score": 0.861,
      "start": "SPL gene",
      "end": "18 SPL genes in rice",
      "bridge_entities": [],
      "hops": [
        {
          "hop_index": 0,
          "from_id": "cent_spl", "from_name": "SPL gene",
          "to_id": "cent_oryza", "to_name": "Oryza sativa",
          "source": "SPL gene", "relation": "characterized_in", "target": "Oryza sativa",
          "source_type": "gene_family", "target_type": "species",
          "relation_category": "characterized_in",
          "assertion_id": "cass_d12f62f9abffbd903b97",
          "paper_id": "PMC5488377_12864_2017_Article_3882",
          "pmid": "28655295", "pmcid": "PMC5488377", "doi": "10.1186/s12864-017-3882-4",
          "support_count": 12, "paper_count": 5, "best_score": 0.95
        }
      ]
    }
  ],
  "assertion_anchored_graph_chains": [],
  "degraded_execution": false,
  "subquestion_evidence_groups": [],
  "rerank_audit": [],
  "timings": { "provisional_answer": 0.5, "retrieval": 12.3, "native_graph_chain_retrieval": 70.1, "total": 91.9 },
  "flow": ["question", "provisional answer", "structured planner", "retrieval", "native_graph_chain_retrieval"]
}