@hongmaple0820/med-scale-research-os 0.43.0

package/dist/workflows/GateParser.js

@@ -0,0 +1,73 @@
+// SCALE Engine — Gate Parser (v0.7.0)
+// 解析验证门控表达式
+export class GateParser {
+    parse(expression) {
+        const expr = expression.trim();
+        if (expr.includes(" and ") || expr.includes(" or ")) {
+            const connector = expr.includes(" and ") ? "and" : "or";
+            const parts = expr.split(connector === "and" ? " and " : " or ");
+            return { type: "compound", connector, expressions: parts.map(p => this.parse(p)) };
+        }
+        if (expr.includes(" == ") || expr.includes(" != ")) {
+            const op = expr.includes(" == ") ? "==" : "!=";
+            const [field, value] = expr.split(" " + op + " ");
+            return { type: "status_check", field: field.trim(), operator: op, value: value.trim() };
+        }
+        const compMatch = expr.match(/([a-zA-Z_]+)\s*(<=|>=|<|>|==)\s*([0-9.]+|[a-zA-Z_]+)/);
+        if (compMatch)
+            return { type: "comparison", field: compMatch[1], operator: compMatch[2], value: parseFloat(compMatch[3]) || compMatch[3] };
+        if (expr.includes(" pass") || expr.includes(" fails")) {
+            const cmd = expr.replace(" pass", "").replace(" fails", "").trim();
+            return { type: "command_check", command: cmd };
+        }
+        if (expr.includes("approval") || expr.includes("human"))
+            return { type: "approval_check" };
+        return { type: "comparison", field: "unknown", operator: "==", value: "true" };
+    }
+    async evaluate(expr, ctx) {
+        if (expr.type === "comparison")
+            return this.evalComparison(expr, ctx);
+        if (expr.type === "status_check")
+            return this.evalStatus(expr, ctx);
+        if (expr.type === "command_check")
+            return this.evalCommand(expr, ctx);
+        if (expr.type === "approval_check")
+            return { passed: false, expression: "human approval", evaluated: expr, reason: "Requires human approval" };
+        if (expr.type === "compound")
+            return this.evalCompound(expr, ctx);
+        return { passed: false, expression: "", evaluated: expr, reason: "Unknown type" };
+    }
+    async evaluateString(expr, ctx) {
+        return this.evaluate(this.parse(expr), ctx);
+    }
+    evalComparison(expr, ctx) {
+        if (!ctx.artifact)
+            return { passed: false, expression: "", evaluated: expr, reason: "No artifact" };
+        const payload = ctx.artifact.payload;
+        const fieldValue = payload[expr.field ?? ""] ?? ctx.artifact[expr.field];
+        const target = expr.value;
+        const passed = expr.operator === "<=" ? fieldValue <= target : expr.operator === "<" ? fieldValue < target : fieldValue === target;
+        return { passed, expression: expr.field + " " + expr.operator + " " + expr.value, evaluated: expr, reason: passed ? "OK" : "Failed" };
+    }
+    evalStatus(expr, ctx) {
+        if (!ctx.artifact)
+            return { passed: false, expression: "", evaluated: expr, reason: "No artifact" };
+        const status = ctx.artifact.status;
+        const passed = expr.operator === "==" ? status === expr.value : status !== expr.value;
+        return { passed, expression: expr.field + " " + expr.operator + " " + expr.value, evaluated: expr, reason: passed ? "OK" : "Mismatch" };
+    }
+    async evalCommand(expr, ctx) {
+        if (!ctx.runCommand)
+            return { passed: false, expression: expr.command ?? "", evaluated: expr, reason: "No runner" };
+        const result = await ctx.runCommand(expr.command ?? "");
+        return { passed: result.success, expression: expr.command + " pass", evaluated: expr, reason: result.success ? "OK" : result.output };
+    }
+    async evalCompound(expr, ctx) {
+        if (!expr.expressions)
+            return { passed: false, expression: "", evaluated: expr, reason: "No sub-expr" };
+        const results = await Promise.all(expr.expressions.map(e => this.evaluate(e, ctx)));
+        const passed = expr.connector === "and" ? results.every(r => r.passed) : results.some(r => r.passed);
+        return { passed, expression: expr.connector ?? "and", evaluated: expr, reason: passed ? "All OK" : "Some failed" };
+    }
+}
+//# sourceMappingURL=GateParser.js.map

package/dist/workflows/GateParser.js.map

@@ -0,0 +1 @@
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package/dist/workflows/WorkflowExecutor.d.ts

@@ -0,0 +1,56 @@
+import type { WorkflowPreset } from "../artifact/types.js";
+import type { IEventBus } from "../core/eventBus.js";
+import type { IArtifactStore } from "../artifact/store.js";
+import { GateResult } from "./GateParser.js";
+export interface WorkflowSession {
+    id: string;
+    presetId: string;
+    presetName: string;
+    currentStep: number;
+    totalSteps: number;
+    status: "running" | "paused" | "completed" | "failed" | "blocked";
+    blockingReason?: string;
+    verifiedSteps: number[];
+    stepHistory: StepHistoryEntry[];
+    startedAt: number;
+    pausedAt?: number;
+    completedAt?: number;
+    context: Record<string, unknown>;
+}
+export interface StepHistoryEntry {
+    stepId: string;
+    stepIndex: number;
+    action: string;
+    status: "pending" | "running" | "verified" | "failed" | "skipped";
+    startedAt: number;
+    completedAt?: number;
+    output?: unknown;
+    error?: string;
+    gateResult?: GateResult;
+}
+export interface IWorkflowExecutor {
+    start(preset: WorkflowPreset, context: Record<string, unknown>): Promise<WorkflowSession>;
+    getStatus(sessionId: string): Promise<WorkflowSession | null>;
+    pause(sessionId: string, reason?: string): Promise<void>;
+    resume(sessionId: string): Promise<void>;
+    executeStep(sessionId: string, stepIndex?: number): Promise<StepHistoryEntry>;
+    runAll(sessionId: string): Promise<WorkflowSession>;
+    getHistory(sessionId: string): Promise<StepHistoryEntry[]>;
+}
+export declare class WorkflowExecutor implements IWorkflowExecutor {
+    private sessions;
+    private gateParser;
+    private eventBus;
+    private store;
+    constructor(eventBus: IEventBus, store: IArtifactStore);
+    start(preset: WorkflowPreset, context: Record<string, unknown>): Promise<WorkflowSession>;
+    getStatus(sessionId: string): Promise<WorkflowSession | null>;
+    pause(sessionId: string, reason?: string): Promise<void>;
+    resume(sessionId: string): Promise<void>;
+    executeStep(sessionId: string, stepIndex?: number): Promise<StepHistoryEntry>;
+    runAll(sessionId: string): Promise<WorkflowSession>;
+    getHistory(sessionId: string): Promise<StepHistoryEntry[]>;
+    private executeAction;
+    private getPresetStep;
+    private getRelatedArtifact;
+}

package/dist/workflows/WorkflowExecutor.js

@@ -0,0 +1,143 @@
+// SCALE Engine — Workflow Executor (v0.7.0)
+// 工作流执行器：执行预设工作流步骤
+import { GateParser } from "./GateParser.js";
+import { logger } from "../core/logger.js";
+export class WorkflowExecutor {
+    constructor(eventBus, store) {
+        this.sessions = new Map();
+        this.gateParser = new GateParser();
+        this.eventBus = eventBus;
+        this.store = store;
+    }
+    async start(preset, context) {
+        const session = {
+            id: `WF-${Date.now()}`,
+            presetId: preset.id,
+            presetName: preset.name,
+            currentStep: 0,
+            totalSteps: preset.steps.length,
+            status: "running",
+            verifiedSteps: [],
+            stepHistory: preset.steps.map((s, i) => ({
+                stepId: s.stepId, stepIndex: i, action: s.action, status: "pending", startedAt: 0
+            })),
+            startedAt: Date.now(),
+            context,
+        };
+        this.sessions.set(session.id, session);
+        this.eventBus.emit("workflow.started", { sessionId: session.id, presetId: preset.id });
+        logger.info({ sessionId: session.id, presetId: preset.id }, "Workflow started");
+        return session;
+    }
+    async getStatus(sessionId) {
+        return this.sessions.get(sessionId) ?? null;
+    }
+    async pause(sessionId, reason) {
+        const session = this.sessions.get(sessionId);
+        if (!session)
+            return;
+        session.status = "paused";
+        session.pausedAt = Date.now();
+        session.blockingReason = reason;
+        this.eventBus.emit("workflow.paused", { sessionId, reason });
+        logger.info({ sessionId, reason }, "Workflow paused");
+    }
+    async resume(sessionId) {
+        const session = this.sessions.get(sessionId);
+        if (!session || session.status !== "paused")
+            return;
+        session.status = "running";
+        session.pausedAt = undefined;
+        session.blockingReason = undefined;
+        this.eventBus.emit("workflow.resumed", { sessionId });
+        logger.info({ sessionId }, "Workflow resumed");
+    }
+    async executeStep(sessionId, stepIndex) {
+        const session = this.sessions.get(sessionId);
+        if (!session)
+            throw new Error("Session not found");
+        if (session.status === "paused")
+            throw new Error("Session is paused");
+        const idx = stepIndex ?? session.currentStep;
+        const step = session.stepHistory[idx];
+        if (!step)
+            throw new Error("Step not found");
+        step.status = "running";
+        step.startedAt = Date.now();
+        try {
+            // 执行动作（模拟）
+            step.output = await this.executeAction(session.context, step.action);
+            // 验证门控
+            const presetStep = this.getPresetStep(session.presetId, idx);
+            if (presetStep?.verificationGate) {
+                const gateResult = await this.gateParser.evaluateString(presetStep.verificationGate, {
+                    artifact: await this.getRelatedArtifact(session.context),
+                    runCommand: async (_cmd) => ({ success: true, output: "" })
+                });
+                step.gateResult = gateResult;
+                if (!gateResult.passed) {
+                    step.status = "failed";
+                    step.error = gateResult.reason;
+                    session.status = "blocked";
+                    session.blockingReason = gateResult.reason;
+                    return step;
+                }
+            }
+            step.status = "verified";
+            step.completedAt = Date.now();
+            session.verifiedSteps.push(idx);
+            session.currentStep = idx + 1;
+            if (session.currentStep >= session.totalSteps) {
+                session.status = "completed";
+                session.completedAt = Date.now();
+                this.eventBus.emit("workflow.completed", { sessionId });
+            }
+            return step;
+        }
+        catch (err) {
+            step.status = "failed";
+            step.error = String(err);
+            step.completedAt = Date.now();
+            session.status = "failed";
+            throw err;
+        }
+    }
+    async runAll(sessionId) {
+        const session = this.sessions.get(sessionId);
+        if (!session)
+            throw new Error("Session not found");
+        for (let i = 0; i < session.totalSteps; i++) {
+            if (session.status === "blocked" || session.status === "failed")
+                break;
+            await this.executeStep(sessionId, i);
+        }
+        return session;
+    }
+    async getHistory(sessionId) {
+        const session = this.sessions.get(sessionId);
+        return session?.stepHistory ?? [];
+    }
+    async executeAction(_context, action) {
+        // 模拟执行，实际由 Agent 或 CLI 处理
+        if (action.startsWith("scale "))
+            return { command: action, executed: true };
+        return { action, result: "simulated" };
+    }
+    getPresetStep(presetId, stepIndex) {
+        // 从 presets.ts 导入的预设中获取 - 简化版本
+        const presets = {
+            "basic-dev": [{ stepId: "explore", action: "explore", isMandatory: true }],
+            "tdd-dev": [{ stepId: "explore", action: "explore", isMandatory: true }],
+            "bug-fix": [{ stepId: "reproduce", action: "reproduce", isMandatory: true }],
+        };
+        return presets[presetId]?.[stepIndex];
+    }
+    async getRelatedArtifact(context) {
+        const artifactId = context.artifactId;
+        if (!artifactId)
+            return undefined;
+        const artifact = await this.store.get(artifactId);
+        return artifact ?? undefined;
+    }
+}
+//# sourceMappingURL=WorkflowExecutor.js.map

package/dist/workflows/WorkflowExecutor.js.map

@@ -0,0 +1 @@
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package/dist/workflows/WorkflowOrchestrator.d.ts

@@ -0,0 +1,81 @@
+import type { WorkflowDefinition, WorkflowExecutionResult } from '../agents/types.js';
+import { AgentPool } from '../agents/AgentPool.js';
+import { AgentDispatcher } from '../agents/AgentDispatcher.js';
+import { PythonBridge } from '../bridge/PythonBridge.js';
+import type { PythonBridgeConfig } from '../bridge/types.js';
+/**
+ * WorkflowOrchestrator — 工作流编排器
+ *
+ * 核心功能：
+ * - 解析 YAML WorkflowDefinition
+ * - 构建 DAG 执行图
+ * - 并行执行无依赖步骤
+ * - 管理步骤状态和输出变量
+ * - 医学研究步骤通过 PythonBridge 调用 Python 分析引擎
+ */
+export declare class WorkflowOrchestrator {
+    private dagBuilder;
+    private agentPool;
+    private dispatcher;
+    private pythonBridge;
+    private outputs;
+    private bridgeResponses;
+    constructor(agentPool: AgentPool, dispatcher: AgentDispatcher);
+    /**
+     * 启用 PythonBridge — 医学研究工作流必需
+     *
+     * @param config 桥接配置（部分即可，缺省值自动补全）
+     */
+    enablePythonBridge(config?: Partial<PythonBridgeConfig>): void;
+    /**
+     * 获取 PythonBridge 实例（如已启用）
+     */
+    getPythonBridge(): PythonBridge | null;
+    /**
+     * 执行工作流
+     * @param workflow Workflow 定义
+     * @returns 执行结果
+     */
+    execute(workflow: WorkflowDefinition): Promise<WorkflowExecutionResult>;
+    /**
+     * 执行单个步骤
+     *
+     * v0.11.0: 医学研究步骤 (role 以 "medical/" 开头) 通过 PythonBridge 执行
+     */
+    private executeStep;
+    /**
+     * 执行医学研究步骤 — 通过 PythonBridge 调用 Python 分析引擎
+     *
+     * step.id 映射到 AnalysisStage:
+     *   'expression'     → Stage 1: 表达分析
+     *   'screening'      → Stage 2: 靶点筛选
+     *   'deep_research'  → Stage 3: 深度调研
+     *   'business'       → Stage 4: 商业规划
+     */
+    private _executeMedicalStep;
+    /**
+     * 构建医学研究阶段输入参数
+     *
+     * 从 workflow context 和前序阶段的输出变量中提取参数
+     */
+    private _buildMedicalStageInput;
+    /**
+     * 解析变量（{{output_name}} → 实际值）
+     */
+    private resolveVariables;
+    /**
+     * 模拟执行（实际应调用 LLM）
+     * TODO: 集成真实 LLM 调用
+     */
+    private simulateExecution;
+    /**
+     * 获取输出变量
+     */
+    getOutput(name: string): string | undefined;
+    /**
+     * 清除输出变量
+     */
+    clearOutputs(): void;
+}
+/** 创建 WorkflowOrchestrator 实例 */
+export declare function createWorkflowOrchestrator(agentPool: AgentPool, dispatcher: AgentDispatcher): WorkflowOrchestrator;