helixlife-expert-cli 0.1.0

package/cli/dist/modules/fund/clinical/commands/sample-size.js

@@ -0,0 +1,164 @@
+import { createFormatLogger, helixlifeError, helixlifeErrorCode, printOutput, } from "../../../../core/index.js";
+import { wrapWorkbenchResult } from "../../../shared/result-wrapper.js";
+import { CLINICAL_EXECUTE_API_PATH, CLINICAL_SAMPLE_CALCULATION_APP_ID, CLINICAL_WORKFLOW_APP_TYPE, } from "../constants.js";
+import { buildSampleParameterTable, buildSampleSizeWorkflowInputs, calculationParametersToItems, fetchCalculationParametersTree, getNextCategoryOptions, initialSampleParameterValues, resolveCalculationCategoryPath, validateSampleParameters, } from "../sample-size.js";
+import { readClinicalStringMap } from "../command-utils.js";
+import { buildClinicalWorkflowBody } from "../apps.js";
+import { streamClinicalWorkflow } from "../sse-utils.js";
+import { canEditFourElementsDesign } from "../four-elements.js";
+import { invalidateClinicalPrecheck, requireClinicalSession, updateClinicalSession, } from "../session-cache.js";
+const SAMPLE_OPTION_DISPLAY = {
+    preserveOrder: true,
+    forbidRecommendLabel: true,
+    useLabelAsIs: true,
+};
+export async function runSampleSizeParameters(options) {
+    const format = options.format ?? "markdown";
+    const path = options.path?.map((value) => value.trim()).filter(Boolean) ?? [];
+    const roots = await fetchCalculationParametersTree();
+    const resolved = resolveCalculationCategoryPath(roots, path);
+    if (resolved.nodes.length !== path.length) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "样本量分类路径无效，请按 parameters 返回的 id 逐级选择");
+    }
+    const nextOptions = getNextCategoryOptions(roots, path);
+    const items = resolved.leaf
+        ? calculationParametersToItems(resolved.leaf.cr_calculation_parameters ?? [])
+        : [];
+    const defaults = initialSampleParameterValues(items);
+    const parameterTable = resolved.leaf
+        ? buildSampleParameterTable(items, defaults)
+        : undefined;
+    const result = {
+        status: "sample_parameters_ready",
+        nextAction: resolved.leaf
+            ? "fill_sample_parameters"
+            : "select_sample_category",
+        selectedPath: resolved.nodes.map((node) => ({
+            id: node.id,
+            label: node.name,
+        })),
+        level: path.length + (resolved.leaf ? 0 : 1),
+        options: nextOptions,
+        optionDisplay: SAMPLE_OPTION_DISPLAY,
+        parameters: items,
+        defaults,
+        ...(parameterTable ? { parameterTable } : {}),
+    };
+    if (format === "json") {
+        printOutput(wrapWorkbenchResult(result, {
+            step: "sample-size",
+            subType: "clinical",
+        }), "json");
+        return;
+    }
+    const log = createFormatLogger(format);
+    if (resolved.leaf && parameterTable) {
+        log(`\n样本量场景：${resolved.nodes.map((node) => node.name).join(" → ")}\n`);
+        log("| 计算参数 | 参数解释 | 参数设定值 |");
+        log("| --- | --- | --- |");
+        for (const row of parameterTable.rows) {
+            log(`| ${row.计算参数} | ${row.参数解释 || "-"} | ${row.参数设定值 || "-"} |`);
+        }
+    }
+    else {
+        log(`\n请选择第 ${path.length + 1} 级分类（按接口顺序原样展示，禁止加推荐）：\n`);
+        for (const option of nextOptions) {
+            log(`- ${option.label} (${option.id})${option.description ? `：${option.description}` : ""}`);
+        }
+    }
+}
+export async function runCalculateSampleSize(options) {
+    const format = options.format ?? "markdown";
+    const path = options.path?.map((value) => value.trim()).filter(Boolean) ?? [];
+    if (!path.length || !options.paramsFile) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "请提供完整 --path 和 --params-file");
+    }
+    const session = await requireClinicalSession(options.sessionId);
+    const roots = await fetchCalculationParametersTree();
+    const resolved = resolveCalculationCategoryPath(roots, path);
+    if (resolved.nodes.length !== path.length || !resolved.leaf) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "样本量分类路径必须指向含计算参数的叶子分类");
+    }
+    const items = calculationParametersToItems(resolved.leaf.cr_calculation_parameters ?? []);
+    const values = await readClinicalStringMap(options.paramsFile, "样本量参数文件");
+    const errors = validateSampleParameters(items, values);
+    if (Object.keys(errors).length > 0) {
+        const result = {
+            status: "validation_failed",
+            nextAction: "fix_inputs",
+            errors,
+            firstErrorMessage: Object.entries(errors)[0]
+                ? `${Object.entries(errors)[0][0]}：${Object.entries(errors)[0][1]}`
+                : "",
+        };
+        if (format === "json") {
+            printOutput(wrapWorkbenchResult(result, {
+                step: "sample-size",
+                subType: "clinical",
+            }, { sessionId: session.sessionId }), "json");
+        }
+        else {
+            const log = createFormatLogger(format);
+            log("\n样本量参数校验失败：");
+            for (const [key, message] of Object.entries(errors)) {
+                log(`- ${key}：${message}`);
+            }
+        }
+        return;
+    }
+    const labels = resolved.nodes.map((node) => node.name);
+    const inputs = buildSampleSizeWorkflowInputs(items, values, labels);
+    const body = buildClinicalWorkflowBody({
+        appId: CLINICAL_SAMPLE_CALCULATION_APP_ID,
+        appName: "样本量计算",
+        appType: CLINICAL_WORKFLOW_APP_TYPE,
+        inputs,
+    });
+    const stream = await streamClinicalWorkflow({
+        path: CLINICAL_EXECUTE_API_PATH,
+        body,
+        format,
+        startLabel: "正在计算样本量...",
+        progressLabel: "样本量计算中",
+        finishLabel: "样本量计算完成",
+        failureMessage: "样本量计算失败，请稍后重试",
+        emptyMessage: "样本量计算结果为空",
+        allowEmptyText: true,
+    });
+    const outputs = stream.outputs ?? {};
+    const resultText = String(outputs.result ?? "").trim();
+    const paramText = String(outputs.param_text ?? "").trim();
+    const reference = String(outputs.reference ?? "").trim();
+    const rSource = String(outputs.R_source ?? "").trim();
+    if (!resultText) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_RESPONSE, "样本量工作流未返回 result");
+    }
+    const sampleParam = `${resultText}\n${rSource}\n${paramText}`.trim();
+    const draft = {
+        ...session.draft,
+        sample: resultText,
+        sampleParam,
+    };
+    await updateClinicalSession(session, invalidateClinicalPrecheck(session, draft));
+    const result = {
+        status: "sample_calculated",
+        nextAction: "review_or_precheck",
+        categoryPath: labels,
+        sample: resultText,
+        sampleParam,
+        reference,
+        rSource,
+        designEditableFields: draft.designEditableFields,
+        canEditDesign: canEditFourElementsDesign(draft),
+    };
+    if (format === "json") {
+        printOutput(wrapWorkbenchResult(result, { step: "sample-size", subType: "clinical" }, {
+            sessionId: session.sessionId,
+            workflowRunId: stream.workflowRunId,
+            cacheReady: true,
+        }), "json");
+        return;
+    }
+    createFormatLogger(format)(`\n## 样本量计算\n\n${resultText}\n`);
+}
+//# sourceMappingURL=sample-size.js.map

package/cli/dist/modules/fund/clinical/commands/sample-size.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/topic-evaluation-create.d.ts

@@ -0,0 +1,25 @@
+import { type OutputFormat } from "../../../../core/index.js";
+import { type ClinicalStep1NextAction, type ClinicalStep1Status } from "../constants.js";
+export interface CreateTopicEvaluationOptions {
+    inputsFile?: string;
+    inputs?: string;
+    researchObjective?: string;
+    yes?: boolean;
+    format?: OutputFormat;
+}
+export interface TopicEvaluationCreateResult {
+    status: ClinicalStep1Status;
+    nextAction: ClinicalStep1NextAction;
+    researchObjective: string;
+    inputs: Record<string, string>;
+    outcome?: "success" | "failed";
+    content?: string;
+    title?: string;
+    errors?: Record<string, string>;
+    firstErrorMessage?: string;
+}
+/**
+ * 临床选题评估完整流程（Step1）
+ */
+export declare function runCreateTopicEvaluation(options?: CreateTopicEvaluationOptions): Promise<void>;
+//# sourceMappingURL=topic-evaluation-create.d.ts.map

package/cli/dist/modules/fund/clinical/commands/topic-evaluation-create.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/topic-evaluation-create.js

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+// Step1 选题评估：采集表单 → 校验 → 调预检工作流（topic_evaluation）→ 返回预检结果
+// 对齐源码 helix-workbench-platform/src/pages/ClinicalTopicEvaluation.tsx
+import { helixlifeError, helixlifeErrorCode, isInteractiveTerminal, printOutput, createInteractiveInterface, askOptionWithRl, createFormatLogger, } from "../../../../core/index.js";
+import { wrapWorkbenchResult } from "../../../shared/result-wrapper.js";
+import { CLINICAL_TOPIC_EVALUATION_APP_ID, CLINICAL_TOPIC_EVALUATION_APP_TYPE, CLINICAL_EXECUTE_API_PATH, RESEARCH_OBJECTIVE_KEY, YES_NO_SEGMENTED_FIELD_KEYS, normalizeYesNoFieldValue, parseClinicalResearchObjective, } from "../constants.js";
+import { fetchClinicalTopicEvaluationFieldsWithFallback, } from "../parameters.js";
+import { applyTopicEvaluationDisplayOrder, buildTopicEvaluationTitle, getEffectiveFieldRequired, getEffectiveSelectOptions, getFieldDisplayName, getTopicEvaluationFieldPlaceholder, normalizeSingleEffectiveSelectValues, pickNonEmptyTopicEvaluationFieldValues, shouldShowField, validateTopicEvaluationForm, parseTopicEvaluationOutputs, } from "../form-rules.js";
+import { buildClinicalWorkflowBody } from "../apps.js";
+import { streamClinicalWorkflow } from "../sse-utils.js";
+import { readClinicalStringMap } from "../command-utils.js";
+function printStep1Json(data, handoff) {
+    printOutput(wrapWorkbenchResult(data, { step: "topic-evaluation", subType: "clinical" }, handoff), "json");
+}
+/** 读取 inputs JSON 文件 */
+async function readInputsFile(path) {
+    return readClinicalStringMap(path, " inputs 文件");
+}
+/** 解析内联 inputs JSON */
+function parseInlineInputs(raw) {
+    let parsed;
+    try {
+        parsed = JSON.parse(raw);
+    }
+    catch {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "--inputs 不是合法 JSON");
+    }
+    if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "--inputs 须为 JSON 对象");
+    }
+    const result = {};
+    for (const [key, value] of Object.entries(parsed)) {
+        result[key] = value == null ? "" : String(value);
+    }
+    return result;
+}
+/** 交互式逐字段采集 */
+async function promptFields(fields, initialInputs) {
+    const inputs = { ...initialInputs };
+    const researchObjective = inputs[RESEARCH_OBJECTIVE_KEY];
+    const assessPrognosis = inputs["Assess_prognosis"];
+    const ordered = applyTopicEvaluationDisplayOrder(fields, researchObjective);
+    const visible = ordered.filter((field) => shouldShowField(field.key, inputs, researchObjective, assessPrognosis));
+    const rl = createInteractiveInterface();
+    try {
+        for (const field of visible) {
+            const effectiveOptions = getEffectiveSelectOptions(field.key, field, inputs);
+            const displayName = getFieldDisplayName(field, researchObjective);
+            const isYesNo = YES_NO_SEGMENTED_FIELD_KEYS.has(field.key);
+            if (field.type === "select" || isYesNo) {
+                const options = isYesNo ? ["是", "否"] : effectiveOptions;
+                if (options.length === 0) {
+                    // 无可选选项，跳过
+                    continue;
+                }
+                if (options.length === 1) {
+                    inputs[field.key] = options[0];
+                    continue;
+                }
+                const currentValue = isYesNo && inputs[field.key]
+                    ? normalizeYesNoFieldValue(inputs[field.key])
+                    : inputs[field.key] || options[0] || "";
+                const selected = await askOptionWithRl(rl, displayName, options, currentValue, (_value, index) => `${index + 1}) ${options[index]}`);
+                inputs[field.key] = selected;
+                // 选中 Research_Objective 后，重新计算后续显隐与排序
+                if (field.key === RESEARCH_OBJECTIVE_KEY) {
+                    return promptFields(fields, inputs);
+                }
+            }
+            else {
+                // paragraph / string / number：自由输入
+                const placeholder = getTopicEvaluationFieldPlaceholder(field.key, researchObjective);
+                const required = getEffectiveFieldRequired(field, inputs, true);
+                const prompt = `${displayName}${required ? "（必填）" : "（非必填）"}${placeholder ? ` [${placeholder}]` : ""}\n> `;
+                const answer = (await rl.question(prompt)).trim();
+                inputs[field.key] = answer;
+            }
+        }
+    }
+    finally {
+        rl.close();
+    }
+    return inputs;
+}
+/** 运行预检工作流（topic_evaluation app） */
+async function runPrecheckWorkflow(inputs, format) {
+    const body = buildClinicalWorkflowBody({
+        query: "",
+        inputs: pickNonEmptyTopicEvaluationFieldValues(inputs),
+        appId: CLINICAL_TOPIC_EVALUATION_APP_ID,
+        appName: "选题评估",
+        appType: CLINICAL_TOPIC_EVALUATION_APP_TYPE,
+    });
+    const stream = await streamClinicalWorkflow({
+        path: CLINICAL_EXECUTE_API_PATH,
+        body,
+        format,
+        startLabel: "正在进行选题评估预检，请稍候...",
+        progressLabel: "预检评估中...",
+        finishLabel: "预检完成",
+        failureMessage: "预检失败，请稍后重试",
+        emptyMessage: "预检未返回有效结果，请稍后重试",
+        allowEmptyText: true,
+    });
+    const parsed = parseTopicEvaluationOutputs(stream.outputs ?? {});
+    return {
+        outcome: parsed.outcome,
+        content: parsed.content,
+        workflowRunId: stream.workflowRunId,
+        elapsedTime: stream.elapsedTime,
+    };
+}
+/**
+ * 临床选题评估完整流程（Step1）
+ */
+export async function runCreateTopicEvaluation(options = {}) {
+    const format = options.format ?? "markdown";
+    const interactive = isInteractiveTerminal() && !options.yes;
+    const log = createFormatLogger(format);
+    // 1. 拉取字段定义
+    const { fields, fallback } = await fetchClinicalTopicEvaluationFieldsWithFallback();
+    if (fallback) {
+        log("\n⚠️ 未能从后端拉取选题评估参数，已使用内置字段定义兜底。\n");
+    }
+    // 2. 解析 inputs
+    let inputs = {};
+    if (options.inputsFile && options.inputs) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "不能同时使用 --inputs-file 与 --inputs，请二选一");
+    }
+    if (options.inputsFile) {
+        inputs = await readInputsFile(options.inputsFile);
+    }
+    else if (options.inputs) {
+        inputs = parseInlineInputs(options.inputs);
+    }
+    if (options.researchObjective) {
+        inputs[RESEARCH_OBJECTIVE_KEY] = parseClinicalResearchObjective(options.researchObjective);
+    }
+    // 3. 交互式补齐 / 非交互校验
+    if (interactive) {
+        log("\n=== Step 1: 选题评估 ===\n");
+        inputs = await promptFields(fields, inputs);
+    }
+    // 对齐页面联动：裁剪后只剩一个选项时自动回落到该值。
+    inputs = normalizeSingleEffectiveSelectValues(fields, inputs).values;
+    const researchObjective = inputs[RESEARCH_OBJECTIVE_KEY];
+    if (!researchObjective) {
+        if (interactive) {
+            // 交互模式理论上已采集，兜底
+            throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "缺少研究类别（Research_Objective），请重新填写");
+        }
+        // 非交互：输出校验失败
+        printStep1Json({
+            status: "validation_failed",
+            nextAction: "fix_inputs",
+            researchObjective: "",
+            inputs,
+            errors: { [RESEARCH_OBJECTIVE_KEY]: "缺少必填字段：研究类别（Research_Objective）" },
+            firstErrorMessage: "缺少必填字段：研究类别（Research_Objective）",
+        });
+        return;
+    }
+    // 4. 计算可见字段并校验
+    const ordered = applyTopicEvaluationDisplayOrder(fields, researchObjective);
+    const assessPrognosis = inputs["Assess_prognosis"];
+    const visibleFields = ordered.filter((field) => shouldShowField(field.key, inputs, researchObjective, assessPrognosis));
+    const validationResult = validateTopicEvaluationForm(visibleFields, inputs);
+    if (!validationResult.ok) {
+        if (format === "json") {
+            printStep1Json({
+                status: "validation_failed",
+                nextAction: "fix_inputs",
+                researchObjective,
+                inputs,
+                errors: validationResult.errors,
+                firstErrorMessage: validationResult.firstMessage,
+            });
+        }
+        else {
+            log("\n❌ 校验未通过，无法调用预检工作流：\n");
+            for (const [, msg] of Object.entries(validationResult.errors)) {
+                log(`- ${msg}`);
+            }
+            log("\n请补全上述必填项后重新执行。\n");
+        }
+        return;
+    }
+    const validInputs = validationResult.values;
+    const title = buildTopicEvaluationTitle(validInputs);
+    // 5. 直接调用预检工作流；网页临床流程不创建订单
+    log("\n接口正在处理中，请耐心等待...");
+    const precheck = await runPrecheckWorkflow(validInputs, format);
+    // 6. 输出结果
+    const status = precheck.outcome === "success" ? "precheck_success" : "precheck_failed";
+    const nextAction = precheck.outcome === "success" ? "proceed_to_four_elements" : "revise_inputs";
+    const result = {
+        status,
+        nextAction,
+        researchObjective,
+        inputs: validInputs,
+        outcome: precheck.outcome,
+        content: precheck.content,
+        title,
+    };
+    if (format === "json") {
+        printStep1Json(result, {
+            workflowRunId: precheck.workflowRunId,
+        });
+        return;
+    }
+    if (precheck.outcome === "success") {
+        log("\n✅ 预检成功：无缺失信息，格式与内容审核通过。\n");
+        if (title) {
+            log(`\n${title}\n`);
+        }
+        if (precheck.content?.trim()) {
+            log(`\n${precheck.content}\n`);
+        }
+        log("\n第 1 步（选题评估）已完成，可进入第 2 步：确认四要素。\n");
+    }
+    else {
+        log("\n❌ 预检失败：根据预检分析，当前内容不符合提交规范，请修改后重新预检。\n");
+        if (precheck.content?.trim()) {
+            log(`\n${precheck.content}\n`);
+        }
+        log("\n请调整输入内容后重新执行 topic-evaluation create。\n");
+    }
+}
+//# sourceMappingURL=topic-evaluation-create.js.map

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package/cli/dist/modules/fund/clinical/commands/topic-evaluation-parameters.d.ts

@@ -0,0 +1,45 @@
+import { type OutputFormat } from "../../../../core/index.js";
+import { fieldToParameterItem } from "../parameters.js";
+import { type TopicEvaluationField } from "../constants.js";
+export interface RunTopicEvaluationParametersOptions {
+    format?: OutputFormat;
+}
+export interface TopicEvaluationEffectiveScenario {
+    autoSelected: Record<string, string>;
+    fields: ReturnType<typeof fieldToParameterItem>[];
+}
+export interface TopicEvaluationLinkageDelta {
+    autoSelected: Record<string, string>;
+    optionOverrides: Record<string, string[]>;
+    requiredOverrides: Record<string, boolean>;
+    /** 相对父节点变化的输入框 placeholder（对齐网页） */
+    placeholderOverrides: Record<string, string>;
+    /** 相对父节点变化的展示名（如诊断下 I → 待评价的诊断实验） */
+    nameOverrides: Record<string, string>;
+    /** 相对父节点变化的完整自由文本提问句 */
+    promptOverrides: Record<string, string>;
+}
+export interface TopicEvaluationVisibilityVariant extends TopicEvaluationLinkageDelta {
+    value: string;
+    hiddenFieldKeys: string[];
+    shownFieldKeys: string[];
+}
+export interface TopicEvaluationStudyDesignLinkage extends TopicEvaluationLinkageDelta {
+    value: string;
+    assessPrognosisVariants: TopicEvaluationVisibilityVariant[];
+}
+export interface TopicEvaluationObjectiveLinkage extends TopicEvaluationLinkageDelta {
+    value: string;
+    fieldKeys: string[];
+    studyDesigns: TopicEvaluationStudyDesignLinkage[];
+}
+/**
+ * 一次性预计算网页中的全部固定联动分支，并只输出相对父节点的差量。
+ * Agent 首次拉取后只需在该树中按用户选择向下匹配，不再调用 parameters。
+ */
+export declare function buildTopicEvaluationLinkage(fields: TopicEvaluationField[]): {
+    researchObjectiveOptions: string[];
+    objectives: TopicEvaluationObjectiveLinkage[];
+};
+export declare function runTopicEvaluationParameters(options?: RunTopicEvaluationParametersOptions): Promise<void>;
+//# sourceMappingURL=topic-evaluation-parameters.d.ts.map

package/cli/dist/modules/fund/clinical/commands/topic-evaluation-parameters.d.ts.map

@@ -0,0 +1 @@
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