@hongmaple0820/med-scale-research-os 0.43.0

package/dist/bridge/medicalWorkflows.js.map

@@ -0,0 +1 @@
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package/dist/bridge/types.d.ts

@@ -0,0 +1,381 @@
+import { z } from 'zod';
+/** 桥接协议版本 */
+export declare const BRIDGE_PROTOCOL_VERSION: "scale-analysis-v1";
+/** 默认超时 (5 分钟) */
+export declare const DEFAULT_STAGE_TIMEOUT_MS = 300000;
+/** 最大重试次数 */
+export declare const MAX_RETRIES = 2;
+/** 心跳间隔 (秒) */
+export declare const HEARTBEAT_INTERVAL_S = 30;
+/** 分析阶段标识 */
+export type AnalysisStage = 'expression' | 'screening' | 'deep_research' | 'business';
+/** 所有支持的分析阶段 */
+export declare const ANALYSIS_STAGES: readonly ["expression", "screening", "deep_research", "business"];
+/** 阶段中文标签 */
+export declare const STAGE_LABELS: Record<AnalysisStage, string>;
+/** 阶段 CLI 子命令映射 (→ Python main.py 子命令) */
+export declare const STAGE_CLI_MAP: Record<AnalysisStage, string>;
+/**
+ * 桥接请求 — TS → Python
+ *
+ * 通过 stdin JSON 传递给 Python 进程
+ */
+export interface BridgeRequest {
+    /** 协议版本 */
+    protocol: typeof BRIDGE_PROTOCOL_VERSION;
+    /** 分析阶段 */
+    stage: AnalysisStage;
+    /** 阶段输入参数 */
+    input: StageInput;
+    /** 超时毫秒 */
+    timeout_ms: number;
+    /** 期望的输出 schema 标识 */
+    output_schema: string;
+    /** 请求 ID (用于追踪) */
+    request_id: string;
+}
+/**
+ * 桥接响应 — Python → TS
+ *
+ * Python 进程通过 stdout 输出
+ */
+export interface BridgeResponse {
+    /** 协议版本 */
+    protocol: typeof BRIDGE_PROTOCOL_VERSION;
+    /** 对应的请求 ID */
+    request_id: string;
+    /** 是否成功 */
+    success: boolean;
+    /** 阶段标识 */
+    stage: AnalysisStage;
+    /** 分析结果（成功时） */
+    data?: unknown;
+    /** 错误信息（失败时） */
+    error?: string;
+    /** 错误详情 */
+    error_details?: {
+        type: string;
+        message: string;
+        traceback?: string;
+    };
+    /** 执行耗时 (ms) */
+    duration_ms: number;
+    /** 数据溯源信息 */
+    provenance?: ProvenanceInfo[];
+}
+/** Stage 1: 表达分析输入 */
+export interface ExpressionStageInput {
+    gene_symbol: string;
+    cancer_types: string[];
+    ensg_id?: string;
+}
+/** Stage 2: 靶点筛选输入 */
+export interface ScreeningStageInput {
+    disease: string;
+    exclude_targets?: string[];
+    top_n?: number;
+    normal_tissue_expression?: Record<string, number>;
+}
+/** Stage 3: 深度调研输入 */
+export interface DeepResearchStageInput {
+    target_name: string;
+    ensg_id?: string;
+    disease?: string;
+}
+/** Stage 4: 商业规划输入 */
+export interface BusinessStageInput {
+    target_name: string;
+    disease?: string;
+    modality?: 'small_molecule' | 'antibody' | 'cell_therapy' | 'gene_therapy';
+    risk_level?: 'low' | 'medium' | 'high';
+    /** 前序阶段输出（可选传入） */
+    stage1_data?: unknown;
+    stage2_data?: unknown;
+    stage3_data?: unknown;
+}
+/** 联合类型 — 任意 Stage 输入 */
+export type StageInput = ExpressionStageInput | ScreeningStageInput | DeepResearchStageInput | BusinessStageInput;
+/** Python 桥接配置 */
+export interface PythonBridgeConfig {
+    /** Python 可执行文件路径 */
+    pythonPath: string;
+    /** target-research-platform 目录（含 main.py） */
+    platformDir: string;
+    /** 缓存目录 */
+    cacheDir: string;
+    /** 输出目录 */
+    outputDir: string;
+    /** 默认超时 (ms) */
+    defaultTimeoutMs: number;
+    /** 最大重试次数 */
+    maxRetries: number;
+    /** 环境变量 */
+    env?: Record<string, string>;
+}
+/** 默认桥接配置 */
+export declare const DEFAULT_BRIDGE_CONFIG: PythonBridgeConfig;
+/** 桥接健康状态 */
+export interface BridgeHealthStatus {
+    /** Python 进程是否可用 */
+    pythonAvailable: boolean;
+    /** Python 版本 */
+    pythonVersion?: string;
+    /** target-research-platform 是否存在 */
+    platformExists: boolean;
+    /** 各 API 数据源健康状态 */
+    apiHealth: Record<string, boolean>;
+    /** 上次检查时间 */
+    lastChecked: string;
+}
+/** 桥接执行状态 */
+export type BridgeExecutionStatus = 'pending' | 'running' | 'completed' | 'failed' | 'timeout' | 'cancelled';
+/** 单次桥接执行记录 */
+export interface BridgeExecutionRecord {
+    /** 请求 ID */
+    requestId: string;
+    /** 分析阶段 */
+    stage: AnalysisStage;
+    /** 执行状态 */
+    status: BridgeExecutionStatus;
+    /** 开始时间 */
+    startedAt: number;
+    /** 结束时间 */
+    completedAt?: number;
+    /** 耗时 (ms) */
+    durationMs?: number;
+    /** 重试次数 */
+    retryCount: number;
+    /** 错误信息 */
+    error?: string;
+    /** 检查点数据（用于断点恢复） */
+    checkpoint?: StageCheckpoint;
+}
+/** 阶段检查点 */
+export interface StageCheckpoint {
+    /** 已完成的阶段 */
+    completedStages: AnalysisStage[];
+    /** 各阶段输出快照路径 */
+    stageOutputPaths: Partial<Record<AnalysisStage, string>>;
+    /** 检查点创建时间 */
+    createdAt: number;
+    /** 关联的研究项目 ID */
+    projectId?: string;
+}
+/** 溯源信息 */
+export interface ProvenanceInfo {
+    /** 数据源名称 */
+    source: string;
+    /** API 端点 */
+    endpoint: string;
+    /** 请求参数 */
+    params: Record<string, unknown>;
+    /** 查询时间戳 */
+    timestamp: string;
+    /** 请求哈希 */
+    request_hash: string;
+}
+/** BridgeRequest Zod Schema */
+export declare const BridgeRequestSchema: z.ZodObject<{
+    protocol: z.ZodLiteral<"scale-analysis-v1">;
+    stage: z.ZodEnum<["expression", "screening", "deep_research", "business"]>;
+    input: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+    timeout_ms: z.ZodNumber;
+    output_schema: z.ZodString;
+    request_id: z.ZodString;
+}, "strip", z.ZodTypeAny, {
+    stage: "expression" | "business" | "screening" | "deep_research";
+    input: Record<string, unknown>;
+    protocol: "scale-analysis-v1";
+    timeout_ms: number;
+    output_schema: string;
+    request_id: string;
+}, {
+    stage: "expression" | "business" | "screening" | "deep_research";
+    input: Record<string, unknown>;
+    protocol: "scale-analysis-v1";
+    timeout_ms: number;
+    output_schema: string;
+    request_id: string;
+}>;
+/** BridgeResponse Zod Schema */
+export declare const BridgeResponseSchema: z.ZodObject<{
+    protocol: z.ZodLiteral<"scale-analysis-v1">;
+    request_id: z.ZodString;
+    success: z.ZodBoolean;
+    stage: z.ZodEnum<["expression", "screening", "deep_research", "business"]>;
+    data: z.ZodOptional<z.ZodUnknown>;
+    error: z.ZodOptional<z.ZodString>;
+    error_details: z.ZodOptional<z.ZodObject<{
+        type: z.ZodString;
+        message: z.ZodString;
+        traceback: z.ZodOptional<z.ZodString>;
+    }, "strip", z.ZodTypeAny, {
+        type: string;
+        message: string;
+        traceback?: string | undefined;
+    }, {
+        type: string;
+        message: string;
+        traceback?: string | undefined;
+    }>>;
+    duration_ms: z.ZodNumber;
+    provenance: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        source: z.ZodString;
+        endpoint: z.ZodString;
+        params: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+        timestamp: z.ZodString;
+        request_hash: z.ZodString;
+    }, "strip", z.ZodTypeAny, {
+        timestamp: string;
+        source: string;
+        endpoint: string;
+        params: Record<string, unknown>;
+        request_hash: string;
+    }, {
+        timestamp: string;
+        source: string;
+        endpoint: string;
+        params: Record<string, unknown>;
+        request_hash: string;
+    }>, "many">>;
+}, "strip", z.ZodTypeAny, {
+    success: boolean;
+    stage: "expression" | "business" | "screening" | "deep_research";
+    protocol: "scale-analysis-v1";
+    request_id: string;
+    duration_ms: number;
+    error?: string | undefined;
+    data?: unknown;
+    error_details?: {
+        type: string;
+        message: string;
+        traceback?: string | undefined;
+    } | undefined;
+    provenance?: {
+        timestamp: string;
+        source: string;
+        endpoint: string;
+        params: Record<string, unknown>;
+        request_hash: string;
+    }[] | undefined;
+}, {
+    success: boolean;
+    stage: "expression" | "business" | "screening" | "deep_research";
+    protocol: "scale-analysis-v1";
+    request_id: string;
+    duration_ms: number;
+    error?: string | undefined;
+    data?: unknown;
+    error_details?: {
+        type: string;
+        message: string;
+        traceback?: string | undefined;
+    } | undefined;
+    provenance?: {
+        timestamp: string;
+        source: string;
+        endpoint: string;
+        params: Record<string, unknown>;
+        request_hash: string;
+    }[] | undefined;
+}>;
+/** ExpressionStageInput Zod Schema */
+export declare const ExpressionStageInputSchema: z.ZodObject<{
+    gene_symbol: z.ZodString;
+    cancer_types: z.ZodArray<z.ZodString, "many">;
+    ensg_id: z.ZodOptional<z.ZodString>;
+}, "strip", z.ZodTypeAny, {
+    gene_symbol: string;
+    cancer_types: string[];
+    ensg_id?: string | undefined;
+}, {
+    gene_symbol: string;
+    cancer_types: string[];
+    ensg_id?: string | undefined;
+}>;
+/** ScreeningStageInput Zod Schema */
+export declare const ScreeningStageInputSchema: z.ZodObject<{
+    disease: z.ZodString;
+    exclude_targets: z.ZodOptional<z.ZodArray<z.ZodString, "many">>;
+    top_n: z.ZodOptional<z.ZodNumber>;
+    normal_tissue_expression: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodNumber>>;
+}, "strip", z.ZodTypeAny, {
+    disease: string;
+    exclude_targets?: string[] | undefined;
+    top_n?: number | undefined;
+    normal_tissue_expression?: Record<string, number> | undefined;
+}, {
+    disease: string;
+    exclude_targets?: string[] | undefined;
+    top_n?: number | undefined;
+    normal_tissue_expression?: Record<string, number> | undefined;
+}>;
+/** DeepResearchStageInput Zod Schema */
+export declare const DeepResearchStageInputSchema: z.ZodObject<{
+    target_name: z.ZodString;
+    ensg_id: z.ZodOptional<z.ZodString>;
+    disease: z.ZodOptional<z.ZodString>;
+}, "strip", z.ZodTypeAny, {
+    target_name: string;
+    ensg_id?: string | undefined;
+    disease?: string | undefined;
+}, {
+    target_name: string;
+    ensg_id?: string | undefined;
+    disease?: string | undefined;
+}>;
+/** BusinessStageInput Zod Schema */
+export declare const BusinessStageInputSchema: z.ZodObject<{
+    target_name: z.ZodString;
+    disease: z.ZodOptional<z.ZodString>;
+    modality: z.ZodOptional<z.ZodEnum<["small_molecule", "antibody", "cell_therapy", "gene_therapy"]>>;
+    risk_level: z.ZodOptional<z.ZodEnum<["low", "medium", "high"]>>;
+    stage1_data: z.ZodOptional<z.ZodUnknown>;
+    stage2_data: z.ZodOptional<z.ZodUnknown>;
+    stage3_data: z.ZodOptional<z.ZodUnknown>;
+}, "strip", z.ZodTypeAny, {
+    target_name: string;
+    disease?: string | undefined;
+    modality?: "small_molecule" | "antibody" | "cell_therapy" | "gene_therapy" | undefined;
+    risk_level?: "low" | "medium" | "high" | undefined;
+    stage1_data?: unknown;
+    stage2_data?: unknown;
+    stage3_data?: unknown;
+}, {
+    target_name: string;
+    disease?: string | undefined;
+    modality?: "small_molecule" | "antibody" | "cell_therapy" | "gene_therapy" | undefined;
+    risk_level?: "low" | "medium" | "high" | undefined;
+    stage1_data?: unknown;
+    stage2_data?: unknown;
+    stage3_data?: unknown;
+}>;
+/** 根据 stage 类型获取对应的 Zod Schema */
+export declare function getStageInputSchema(stage: AnalysisStage): z.ZodSchema;
+/** 完整管线请求 */
+export interface FullPipelineRequest {
+    /** 靶点基因名 */
+    target: string;
+    /** 疾病名 */
+    disease: string;
+    /** 癌种代码列表 */
+    cancer_types: string[];
+    /** Ensembl Gene ID (可选) */
+    ensg_id?: string;
+    /** 药物形式 */
+    modality?: 'small_molecule' | 'antibody' | 'cell_therapy' | 'gene_therapy';
+    /** 风险等级 */
+    risk_level?: 'low' | 'medium' | 'high';
+}
+/** 完整管线响应 */
+export interface FullPipelineResponse {
+    success: boolean;
+    target: string;
+    disease: string;
+    stages: Partial<Record<AnalysisStage, BridgeResponse>>;
+    summary: {
+        stages_completed: AnalysisStage[];
+        stages_failed: AnalysisStage[];
+    };
+    duration_ms: number;
+}

package/dist/bridge/types.js

@@ -0,0 +1,113 @@
+// SCALE Engine — Python-TS Bridge Protocol Types (v1.0.0)
+// Python-TS 桥接协议类型定义
+// 协议版本: scale-analysis-v1
+import { z } from 'zod';
+// ============================================================================
+// 1. Bridge Protocol Constants
+// ============================================================================
+/** 桥接协议版本 */
+export const BRIDGE_PROTOCOL_VERSION = 'scale-analysis-v1';
+/** 默认超时 (5 分钟) */
+export const DEFAULT_STAGE_TIMEOUT_MS = 300_000;
+/** 最大重试次数 */
+export const MAX_RETRIES = 2;
+/** 心跳间隔 (秒) */
+export const HEARTBEAT_INTERVAL_S = 30;
+/** 所有支持的分析阶段 */
+export const ANALYSIS_STAGES = ['expression', 'screening', 'deep_research', 'business'];
+/** 阶段中文标签 */
+export const STAGE_LABELS = {
+    expression: '靶点表达全景与预后挖掘',
+    screening: '多维靶点筛选与优先级排序',
+    deep_research: '靶点深度调研与赛道格局分析',
+    business: '商业计划书与里程碑规划',
+};
+/** 阶段 CLI 子命令映射 (→ Python main.py 子命令) */
+export const STAGE_CLI_MAP = {
+    expression: 'stage1',
+    screening: 'stage2',
+    deep_research: 'stage3',
+    business: 'stage4',
+};
+/** 默认桥接配置 */
+export const DEFAULT_BRIDGE_CONFIG = {
+    pythonPath: 'python',
+    platformDir: './target-research-platform',
+    cacheDir: './cache',
+    outputDir: './output',
+    defaultTimeoutMs: DEFAULT_STAGE_TIMEOUT_MS,
+    maxRetries: MAX_RETRIES,
+};
+// ============================================================================
+// 9. Zod Schemas — 运行时校验
+// ============================================================================
+/** BridgeRequest Zod Schema */
+export const BridgeRequestSchema = z.object({
+    protocol: z.literal(BRIDGE_PROTOCOL_VERSION),
+    stage: z.enum(ANALYSIS_STAGES),
+    input: z.record(z.unknown()),
+    timeout_ms: z.number().positive(),
+    output_schema: z.string().min(1),
+    request_id: z.string().min(1),
+});
+/** BridgeResponse Zod Schema */
+export const BridgeResponseSchema = z.object({
+    protocol: z.literal(BRIDGE_PROTOCOL_VERSION),
+    request_id: z.string(),
+    success: z.boolean(),
+    stage: z.enum(ANALYSIS_STAGES),
+    data: z.unknown().optional(),
+    error: z.string().optional(),
+    error_details: z.object({
+        type: z.string(),
+        message: z.string(),
+        traceback: z.string().optional(),
+    }).optional(),
+    duration_ms: z.number().nonnegative(),
+    provenance: z.array(z.object({
+        source: z.string(),
+        endpoint: z.string(),
+        params: z.record(z.unknown()),
+        timestamp: z.string(),
+        request_hash: z.string(),
+    })).optional(),
+});
+/** ExpressionStageInput Zod Schema */
+export const ExpressionStageInputSchema = z.object({
+    gene_symbol: z.string().min(1),
+    cancer_types: z.array(z.string()).min(1),
+    ensg_id: z.string().optional(),
+});
+/** ScreeningStageInput Zod Schema */
+export const ScreeningStageInputSchema = z.object({
+    disease: z.string().min(1),
+    exclude_targets: z.array(z.string()).optional(),
+    top_n: z.number().int().positive().optional(),
+    normal_tissue_expression: z.record(z.number()).optional(),
+});
+/** DeepResearchStageInput Zod Schema */
+export const DeepResearchStageInputSchema = z.object({
+    target_name: z.string().min(1),
+    ensg_id: z.string().optional(),
+    disease: z.string().optional(),
+});
+/** BusinessStageInput Zod Schema */
+export const BusinessStageInputSchema = z.object({
+    target_name: z.string().min(1),
+    disease: z.string().optional(),
+    modality: z.enum(['small_molecule', 'antibody', 'cell_therapy', 'gene_therapy']).optional(),
+    risk_level: z.enum(['low', 'medium', 'high']).optional(),
+    stage1_data: z.unknown().optional(),
+    stage2_data: z.unknown().optional(),
+    stage3_data: z.unknown().optional(),
+});
+/** 根据 stage 类型获取对应的 Zod Schema */
+export function getStageInputSchema(stage) {
+    switch (stage) {
+        case 'expression': return ExpressionStageInputSchema;
+        case 'screening': return ScreeningStageInputSchema;
+        case 'deep_research': return DeepResearchStageInputSchema;
+        case 'business': return BusinessStageInputSchema;
+    }
+}
+//# sourceMappingURL=types.js.map

package/dist/bridge/types.js.map

@@ -0,0 +1 @@
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package/dist/cache/ScanCache.d.ts

@@ -0,0 +1,41 @@
+export interface CacheEntry {
+    key: string;
+    gateId: string;
+    result: unknown;
+    passed: boolean;
+    durationMs: number;
+    fileHashes: Record<string, string>;
+    createdAt: string;
+    ttl: number;
+}
+export interface CacheStats {
+    totalEntries: number;
+    hits: number;
+    misses: number;
+    hitRate: number;
+    bytesUsed: number;
+}
+export declare class ScanCache {
+    private cacheDir;
+    private hitCount;
+    private missCount;
+    constructor(projectDir?: string);
+    /**
+     * Compute a cache key from file paths and their content hashes.
+     */
+    computeKey(files: Record<string, string>): string;
+    /**
+     * Get a cached gate result. Returns null on miss or expiry.
+     */
+    get(gateId: string, key: string): CacheEntry | null;
+    /**
+     * Store a gate result in cache.
+     */
+    set(gateId: string, key: string, result: unknown, passed: boolean, durationMs: number, fileHashes: Record<string, string>, ttlSeconds?: number): void;
+    stats(): CacheStats;
+    clear(): number;
+    private listEntries;
+    /** Compute the hash of file contents for changed-file detection */
+    hashFiles(filePaths: string[]): Record<string, string>;
+    private sha256;
+}

package/dist/cache/ScanCache.js

@@ -0,0 +1,120 @@
+import { createHash } from 'node:crypto';
+import { existsSync, mkdirSync, readFileSync, writeFileSync, unlinkSync } from 'node:fs';
+import { join } from 'node:path';
+export class ScanCache {
+    constructor(projectDir = process.cwd()) {
+        this.hitCount = 0;
+        this.missCount = 0;
+        this.cacheDir = join(projectDir, '.scale', 'cache', 'scans');
+        if (!existsSync(this.cacheDir))
+            mkdirSync(this.cacheDir, { recursive: true });
+    }
+    /**
+     * Compute a cache key from file paths and their content hashes.
+     */
+    computeKey(files) {
+        const sorted = Object.entries(files).sort(([a], [b]) => a.localeCompare(b));
+        const payload = sorted.map(([path, content]) => `${path}:${this.sha256(content)}`).join('\n');
+        return this.sha256(payload);
+    }
+    /**
+     * Get a cached gate result. Returns null on miss or expiry.
+     */
+    get(gateId, key) {
+        const entryPath = join(this.cacheDir, `${gateId}-${key}.json`);
+        if (!existsSync(entryPath)) {
+            this.missCount++;
+            return null;
+        }
+        try {
+            const entry = JSON.parse(readFileSync(entryPath, 'utf-8'));
+            const age = (Date.now() - new Date(entry.createdAt).getTime()) / 1000;
+            if (age > entry.ttl) {
+                // Expired -- clean up
+                try {
+                    unlinkSync(entryPath);
+                }
+                catch { }
+                this.missCount++;
+                return null;
+            }
+            this.hitCount++;
+            return entry;
+        }
+        catch {
+            this.missCount++;
+            return null;
+        }
+    }
+    /**
+     * Store a gate result in cache.
+     */
+    set(gateId, key, result, passed, durationMs, fileHashes, ttlSeconds = 300) {
+        const entry = {
+            key,
+            gateId,
+            result,
+            passed,
+            durationMs,
+            fileHashes,
+            createdAt: new Date().toISOString(),
+            ttl: ttlSeconds,
+        };
+        const entryPath = join(this.cacheDir, `${gateId}-${key}.json`);
+        writeFileSync(entryPath, JSON.stringify(entry, null, 2));
+    }
+    stats() {
+        const entries = existsSync(this.cacheDir) ? this.listEntries() : [];
+        let bytesUsed = 0;
+        for (const e of entries) {
+            try {
+                bytesUsed += readFileSync(join(this.cacheDir, e), 'utf-8').length;
+            }
+            catch { }
+        }
+        return {
+            totalEntries: entries.length,
+            hits: this.hitCount,
+            misses: this.missCount,
+            hitRate: (this.hitCount + this.missCount) > 0 ? this.hitCount / (this.hitCount + this.missCount) : 0,
+            bytesUsed,
+        };
+    }
+    clear() {
+        const entries = this.listEntries();
+        for (const e of entries) {
+            try {
+                unlinkSync(join(this.cacheDir, e));
+            }
+            catch { }
+        }
+        return entries.length;
+    }
+    listEntries() {
+        const { readdirSync } = require('node:fs');
+        try {
+            return readdirSync(this.cacheDir);
+        }
+        catch {
+            return [];
+        }
+    }
+    /** Compute the hash of file contents for changed-file detection */
+    hashFiles(filePaths) {
+        const result = {};
+        for (const fp of filePaths) {
+            try {
+                const content = readFileSync(fp, 'utf-8');
+                result[fp] = this.sha256(content);
+            }
+            catch {
+                result[fp] = 'missing';
+            }
+        }
+        return result;
+    }
+    sha256(input) {
+        return createHash('sha256').update(input).digest('hex').slice(0, 16);
+    }
+}
+//# sourceMappingURL=ScanCache.js.map

package/dist/cache/ScanCache.js.map

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