artifacts/api-server/src/lib/capability/external-knowledge/drug.adapter.ts

/**
 * drug.adapter — 真查 PG drug_nodes / target_nodes / outcome_nodes +
 * drug_targets_protein / drug_affects_outcome / drug_tested_in_trial。
 *
 * 支持过滤参数:
 *   - drug_id      按 drug → 关联 targets / outcomes / trials
 *   - target_id    按 target → 关联 drugs
 *   - outcome_id   按 outcome → 关联 drugs
 *
 * 返回的 KnowledgeItem.payload 带关联强度(confidence)+ source_db。
 */
import { eq, inArray } from "drizzle-orm";
import {
  drugNodes,
  targetNodes,
  outcomeNodes,
  drugTargetsProtein,
  drugAffectsOutcome,
  db,
} from "@workspace/db";
import { enforceBudget } from "./budget-guard.ts";
import { fingerprintParams, recordCall } from "./telemetry.ts";
import type {
  KnowledgeAdapter,
  KnowledgeItem,
  KnowledgeQuery,
  KnowledgeResult,
} from "./types.ts";

interface DrugParams {
  drug_id?: string;
  target_id?: string;
  outcome_id?: string;
}

function readParams(p: Record<string, unknown>): DrugParams {
  return {
    drug_id: typeof p["drug_id"] === "string" ? (p["drug_id"] as string) : undefined,
    target_id: typeof p["target_id"] === "string" ? (p["target_id"] as string) : undefined,
    outcome_id:
      typeof p["outcome_id"] === "string" ? (p["outcome_id"] as string) : undefined,
  };
}

export const drugAdapter: KnowledgeAdapter = {
  kind: "drug_network",
  status: "real",
  async query(q: KnowledgeQuery): Promise<KnowledgeResult> {
    enforceBudget(q.capabilityId, "drug_network");
    const params = readParams(q.params ?? {});
    const limit = Math.min(q.limit ?? 50, 500);
    const fp = fingerprintParams({ ...params, limit });
    const t0 = Date.now();
    let error: string | null = null;
    let items: KnowledgeItem[] = [];

    try {
      if (!params.drug_id && !params.target_id && !params.outcome_id) {
        // 不允许无任何过滤 — 否则一次拉满整张表,昂贵且无意义。
        // 显式 throw 而不是返空,符合反欺骗原则。
        throw new Error(
          "drug.adapter requires at least one of drug_id / target_id / outcome_id",
        );
      }

      // drug_id → 拉相关 target 和 outcome 联表
      if (params.drug_id) {
        const targets = await db
          .select({
            drugId: drugTargetsProtein.drugId,
            targetId: drugTargetsProtein.targetId,
            sourceDb: drugTargetsProtein.sourceDb,
            confidence: drugTargetsProtein.confidence,
            target: targetNodes,
          })
          .from(drugTargetsProtein)
          .leftJoin(
            targetNodes,
            eq(drugTargetsProtein.targetId, targetNodes.targetId),
          )
          .where(eq(drugTargetsProtein.drugId, params.drug_id))
          .limit(limit);

        for (const row of targets) {
          items.push({
            id: `${row.drugId}::${row.targetId}::${row.sourceDb}`,
            score: row.confidence,
            payload: {
              edge_kind: "drug_targets_protein",
              drug_id: row.drugId,
              target_id: row.targetId,
              source_db: row.sourceDb,
              confidence: row.confidence,
              target: row.target,
            },
            origin: "pg:drug_targets_protein",
          });
        }

        const outcomes = await db
          .select({
            drugId: drugAffectsOutcome.drugId,
            outcomeId: drugAffectsOutcome.outcomeId,
            sourceDb: drugAffectsOutcome.sourceDb,
            confidence: drugAffectsOutcome.confidence,
            outcome: outcomeNodes,
          })
          .from(drugAffectsOutcome)
          .leftJoin(
            outcomeNodes,
            eq(drugAffectsOutcome.outcomeId, outcomeNodes.outcomeId),
          )
          .where(eq(drugAffectsOutcome.drugId, params.drug_id))
          .limit(limit);

        for (const row of outcomes) {
          items.push({
            id: `${row.drugId}::${row.outcomeId}::${row.sourceDb}`,
            score: row.confidence,
            payload: {
              edge_kind: "drug_affects_outcome",
              drug_id: row.drugId,
              outcome_id: row.outcomeId,
              source_db: row.sourceDb,
              confidence: row.confidence,
              outcome: row.outcome,
            },
            origin: "pg:drug_affects_outcome",
          });
        }
      }

      // target_id → 反查 drugs,然后用 drug_ids 2-hop 查 outcomes
      if (params.target_id) {
        const drugs = await db
          .select({
            drugId: drugTargetsProtein.drugId,
            targetId: drugTargetsProtein.targetId,
            sourceDb: drugTargetsProtein.sourceDb,
            confidence: drugTargetsProtein.confidence,
            drug: drugNodes,
          })
          .from(drugTargetsProtein)
          .leftJoin(drugNodes, eq(drugTargetsProtein.drugId, drugNodes.drugId))
          .where(eq(drugTargetsProtein.targetId, params.target_id))
          .limit(limit);
        for (const row of drugs) {
          items.push({
            id: `${row.drugId}::${row.targetId}::${row.sourceDb}`,
            score: row.confidence,
            payload: {
              edge_kind: "target_targeted_by_drug",
              drug_id: row.drugId,
              target_id: row.targetId,
              source_db: row.sourceDb,
              confidence: row.confidence,
              drug: row.drug,
            },
            origin: "pg:drug_targets_protein",
          });
        }

        // 2-hop:target → drugs → outcomes(临床上"作用于此 target 的药
        // 都影响哪些 outcome");使用刚查到的 drug_ids 做 IN 过滤,避免
        // 全表扫;调用方可以用 sourceMetadata.tracedDrugIds 复现。
        const tracedDrugIds = Array.from(
          new Set(drugs.map((d) => d.drugId).filter((x): x is string => !!x)),
        );
        if (tracedDrugIds.length > 0) {
          const outcomes = await db
            .select({
              drugId: drugAffectsOutcome.drugId,
              outcomeId: drugAffectsOutcome.outcomeId,
              sourceDb: drugAffectsOutcome.sourceDb,
              confidence: drugAffectsOutcome.confidence,
              outcome: outcomeNodes,
            })
            .from(drugAffectsOutcome)
            .leftJoin(
              outcomeNodes,
              eq(drugAffectsOutcome.outcomeId, outcomeNodes.outcomeId),
            )
            .where(inArray(drugAffectsOutcome.drugId, tracedDrugIds))
            .limit(limit);
          for (const row of outcomes) {
            items.push({
              id: `${row.drugId}::${row.outcomeId}::${row.sourceDb}::via_target`,
              score: row.confidence,
              payload: {
                edge_kind: "target_to_outcome_via_drug",
                target_id: params.target_id,
                drug_id: row.drugId,
                outcome_id: row.outcomeId,
                source_db: row.sourceDb,
                confidence: row.confidence,
                outcome: row.outcome,
              },
              origin: "pg:drug_affects_outcome",
            });
          }
        }
      }

      // outcome_id → 反查 drugs
      if (params.outcome_id) {
        const drugs = await db
          .select({
            drugId: drugAffectsOutcome.drugId,
            outcomeId: drugAffectsOutcome.outcomeId,
            sourceDb: drugAffectsOutcome.sourceDb,
            confidence: drugAffectsOutcome.confidence,
            drug: drugNodes,
          })
          .from(drugAffectsOutcome)
          .leftJoin(drugNodes, eq(drugAffectsOutcome.drugId, drugNodes.drugId))
          .where(eq(drugAffectsOutcome.outcomeId, params.outcome_id))
          .limit(limit);
        for (const row of drugs) {
          items.push({
            id: `${row.drugId}::${row.outcomeId}::${row.sourceDb}`,
            score: row.confidence,
            payload: {
              edge_kind: "outcome_caused_by_drug",
              drug_id: row.drugId,
              outcome_id: row.outcomeId,
              source_db: row.sourceDb,
              confidence: row.confidence,
              drug: row.drug,
            },
            origin: "pg:drug_affects_outcome",
          });
        }
      }
    } catch (err) {
      error = err instanceof Error ? err.message : String(err);
      throw err;
    } finally {
      void recordCall({
        adapter: "drug_network",
        capabilityId: q.capabilityId,
        latencyMs: Date.now() - t0,
        hitCount: items.length,
        cacheHit: null,
        error,
        paramsFingerprint: fp,
      });
    }
    return {
      kind: "drug_network",
      items: items.slice(0, limit),
      cursor: null,
      sourceMetadata: {
        primarySource: "pg:drug_network",
        limit,
        filters: params,
      },
    };
  },
};