helixlife-expert-cli 0.1.0

package/cli/dist/modules/fund/clinical/commands/article-download.js

@@ -0,0 +1,153 @@
+import { mkdir, readFile, writeFile } from "node:fs/promises";
+import { dirname, extname, join } from "node:path";
+import { ApiClient, getDefaultNewideaBaseUrl, getUserDownloadsDir, helixlifeError, helixlifeErrorCode, printOutput, resolveUserPath, sanitizeFilename, } from "../../../../core/index.js";
+import { CLINICAL_CONTENT_PRODUCER, CLINICAL_DOCX_CONVERT_API_PATH, } from "../constants.js";
+import { loadClinicalSession, popClinicalSession, } from "../session-cache.js";
+const DEFAULT_TITLE = "未命名";
+function cleanMarkdownInline(value) {
+    return value
+        .replace(/^\*{1,2}|\*{1,2}$/g, "")
+        .replace(/^项目名称\s*[:：]\s*/, "")
+        .trim();
+}
+/** 对齐网页标题语义：项目名称/标题/Title 优先，否则首个有效 H1。 */
+export function extractClinicalArticleTitle(markdown) {
+    const lines = markdown.split(/\r?\n/);
+    for (let index = 0; index < lines.length; index += 1) {
+        const line = lines[index].trim();
+        if (!line)
+            continue;
+        const labeled = line.match(/^(?:#{1,6}\s*)?(?:项目名称|标题|Title)\s*[:：]\s*(.+)$/i);
+        if (labeled?.[1])
+            return cleanMarkdownInline(labeled[1]);
+        const heading = line.match(/^#(?!#)\s+(.+)$/);
+        if (!heading)
+            continue;
+        const text = cleanMarkdownInline(heading[1]);
+        if (!/^(?:项目名称|标题|Title)$/i.test(text))
+            return text;
+        for (let next = index + 1; next < lines.length; next += 1) {
+            const candidate = lines[next].trim();
+            if (!candidate)
+                continue;
+            if (/^#{1,6}\s+/.test(candidate))
+                break;
+            return cleanMarkdownInline(candidate);
+        }
+    }
+    return DEFAULT_TITLE;
+}
+export function appendClinicalReferences(article, references) {
+    const filtered = references.map((item) => item.trim()).filter(Boolean);
+    if (!filtered.length)
+        return `${article.trim()}\n`;
+    return `${article.trim()}\n\n## 参考文献\n\n${filtered.join("\n")}\n`;
+}
+function toSafeBasename(title) {
+    const safe = sanitizeFilename(title || DEFAULT_TITLE, { maxLength: 80 });
+    return safe.replace(/\.[A-Za-z0-9]{1,8}$/, "") || DEFAULT_TITLE;
+}
+export function resolveClinicalDownloadPaths(output, title) {
+    const filename = `${toSafeBasename(title)}.docx`;
+    let docxPath;
+    if (output) {
+        const resolved = resolveUserPath(output);
+        docxPath = extname(resolved) ? resolved : join(resolved, filename);
+    }
+    else {
+        docxPath = join(getUserDownloadsDir(), filename);
+    }
+    const extension = extname(docxPath);
+    const mdPath = extension
+        ? `${docxPath.slice(0, -extension.length)}.md`
+        : `${docxPath}.md`;
+    return { docxPath, mdPath };
+}
+async function readReferencesFile(path) {
+    if (!path)
+        return [];
+    try {
+        const parsed = JSON.parse(await readFile(resolveUserPath(path), "utf8"));
+        if (!Array.isArray(parsed))
+            throw new Error("顶层必须是 JSON 数组");
+        return parsed
+            .filter((item) => typeof item === "string")
+            .map((item) => item.trim())
+            .filter(Boolean);
+    }
+    catch (error) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `无法读取参考文献文件: ${error.message}`);
+    }
+}
+export async function downloadClinicalArticleDocx(markdown, produceId) {
+    const form = new FormData();
+    form.append("data", new Blob([markdown], { type: "text/plain" }), "blob");
+    form.append("is_aigc", "true");
+    form.append("content_producer", CLINICAL_CONTENT_PRODUCER);
+    form.append("produce_id", produceId);
+    form.append("csl_key", "");
+    const client = new ApiClient();
+    return client.requestBinary(CLINICAL_DOCX_CONVERT_API_PATH, {
+        method: "POST",
+        baseUrl: getDefaultNewideaBaseUrl(),
+        body: form,
+    });
+}
+export async function runDownloadClinicalArticle(options) {
+    if (options.sessionId && options.file) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "--session-id 与 --file 互斥，请二选一");
+    }
+    let article = "";
+    let references = [];
+    let produceId = options.produceId?.trim() ?? "";
+    let consumeSessionId;
+    if (options.sessionId) {
+        const session = await loadClinicalSession(options.sessionId);
+        if (!session?.article?.article) {
+            throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "全文缓存缺失或已清理，请重新生成全文，或通过 --file 提供 Markdown");
+        }
+        article = session.article.article;
+        references = session.article.references;
+        produceId ||= session.article.workflowRunId ?? "";
+        consumeSessionId = session.sessionId;
+    }
+    else if (options.file) {
+        try {
+            article = await readFile(resolveUserPath(options.file), "utf8");
+        }
+        catch (error) {
+            throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `无法读取全文文件: ${error.message}`);
+        }
+        references = await readReferencesFile(options.referencesFile);
+    }
+    else {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "请通过 --session-id 命中全文缓存，或通过 --file 提供 Markdown");
+    }
+    const markdown = appendClinicalReferences(article, references);
+    const title = extractClinicalArticleTitle(markdown);
+    const paths = resolveClinicalDownloadPaths(options.output, title);
+    const { buffer, contentType } = await downloadClinicalArticleDocx(markdown, produceId);
+    await mkdir(dirname(paths.docxPath), { recursive: true });
+    await writeFile(paths.docxPath, buffer);
+    const mdBuffer = Buffer.from(markdown, "utf8");
+    await writeFile(paths.mdPath, mdBuffer);
+    if (consumeSessionId)
+        await popClinicalSession(consumeSessionId);
+    const result = {
+        mdPath: paths.mdPath,
+        mdSize: mdBuffer.byteLength,
+        docxPath: paths.docxPath,
+        docxSize: buffer.byteLength,
+        contentType,
+        filename: `${toSafeBasename(title)}.docx`,
+    };
+    if (options.format === "json") {
+        printOutput(result, "json");
+    }
+    else {
+        console.log(`全文 Markdown 已保存: ${result.mdPath} (${result.mdSize} 字节)`);
+        console.log(`全文 Word 已保存: ${result.docxPath} (${result.docxSize} 字节)`);
+    }
+    return result;
+}
+//# sourceMappingURL=article-download.js.map

package/cli/dist/modules/fund/clinical/commands/article-download.js.map

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

@@ -0,0 +1,7 @@
+import { type OutputFormat } from "../../../../core/index.js";
+export interface CreateFourElementsOptions {
+    inputsFile?: string;
+    format?: OutputFormat;
+}
+export declare function runCreateFourElements(options: CreateFourElementsOptions): Promise<void>;
+//# sourceMappingURL=four-elements-create.d.ts.map

package/cli/dist/modules/fund/clinical/commands/four-elements-create.d.ts.map

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package/cli/dist/modules/fund/clinical/commands/four-elements-create.js

@@ -0,0 +1,81 @@
+import { randomUUID } from "node:crypto";
+import { createFormatLogger, helixlifeError, helixlifeErrorCode, printOutput, } from "../../../../core/index.js";
+import { wrapWorkbenchResult } from "../../../shared/result-wrapper.js";
+import { CLINICAL_EXECUTE_API_PATH, CLINICAL_FOUR_ELEMENTS_APP_IDS, CLINICAL_WORKFLOW_APP_TYPE, parseClinicalResearchObjective, } from "../constants.js";
+import { buildClinicalWorkflowBody } from "../apps.js";
+import { streamClinicalWorkflow } from "../sse-utils.js";
+import { EMPTY_CLINICAL_FOUR_ELEMENTS_DRAFT, canEditFourElementsDesign, mergeClinicalFourElementsDraft, validateFourElementsDraft, } from "../four-elements.js";
+import { readClinicalStringMap } from "../command-utils.js";
+import { saveClinicalSession } from "../session-cache.js";
+export async function runCreateFourElements(options) {
+    const format = options.format ?? "markdown";
+    const log = createFormatLogger(format);
+    if (!options.inputsFile) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "请提供包含 Step1 data.inputs 的 --inputs-file");
+    }
+    const topicInputs = await readClinicalStringMap(options.inputsFile, "Step1 inputs 文件");
+    const researchObjective = parseClinicalResearchObjective(topicInputs.Research_Objective ?? "");
+    const appId = CLINICAL_FOUR_ELEMENTS_APP_IDS[researchObjective];
+    const body = buildClinicalWorkflowBody({
+        appId,
+        appName: `${researchObjective}-四要素校验`,
+        appType: CLINICAL_WORKFLOW_APP_TYPE,
+        inputs: topicInputs,
+    });
+    const stream = await streamClinicalWorkflow({
+        path: CLINICAL_EXECUTE_API_PATH,
+        body,
+        format,
+        startLabel: "正在生成四要素...",
+        progressLabel: "四要素生成中",
+        finishLabel: "四要素生成完成",
+        failureMessage: "四要素生成失败，请稍后重试",
+        emptyMessage: "四要素生成结果为空",
+        allowEmptyText: true,
+    });
+    const draft = mergeClinicalFourElementsDraft(EMPTY_CLINICAL_FOUR_ELEMENTS_DRAFT, stream.outputs ?? {});
+    const missing = validateFourElementsDraft(draft);
+    if (Object.keys(missing).length > 0) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_RESPONSE, `四要素工作流返回不完整：${Object.values(missing).join("；")}`);
+    }
+    const sessionId = randomUUID();
+    const cacheReady = await saveClinicalSession({
+        sessionId,
+        topicInputs,
+        researchObjective,
+        draft,
+        proofread: null,
+        precheckInputs: null,
+    });
+    if (!cacheReady) {
+        throw new helixlifeError(helixlifeErrorCode.REQUEST_FAILED, "四要素已生成，但流程状态保存失败，请重试");
+    }
+    const result = {
+        status: "four_elements_ready",
+        nextAction: "review_four_elements",
+        researchObjective,
+        design: draft.design,
+        purpose: draft.purpose,
+        outcome: draft.outcome,
+        sample: draft.sample,
+        designEditableFields: draft.designEditableFields,
+        canEditDesign: canEditFourElementsDesign(draft),
+    };
+    if (format === "json") {
+        printOutput(wrapWorkbenchResult(result, {
+            step: "four-elements",
+            subType: "clinical",
+        }, {
+            sessionId,
+            workflowRunId: stream.workflowRunId,
+            cacheReady,
+        }), "json");
+        return;
+    }
+    log(`\n## 研究设计\n\n${draft.design}`);
+    log(`\n## 研究目的\n\n${draft.purpose}`);
+    log(`\n## 结局指标\n\n${draft.outcome}`);
+    log(`\n## 样本量计算\n\n${draft.sample}`);
+    log("\n四要素已生成，请确认或修改后进行预检。\n");
+}
+//# sourceMappingURL=four-elements-create.js.map

package/cli/dist/modules/fund/clinical/commands/four-elements-create.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/four-elements-precheck.d.ts

@@ -0,0 +1,7 @@
+import { type OutputFormat } from "../../../../core/index.js";
+export interface PrecheckFourElementsOptions {
+    sessionId?: string;
+    format?: OutputFormat;
+}
+export declare function runPrecheckFourElements(options: PrecheckFourElementsOptions): Promise<void>;
+//# sourceMappingURL=four-elements-precheck.d.ts.map

package/cli/dist/modules/fund/clinical/commands/four-elements-precheck.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/four-elements-precheck.js

@@ -0,0 +1,76 @@
+import { createFormatLogger, printOutput, } from "../../../../core/index.js";
+import { wrapWorkbenchResult } from "../../../shared/result-wrapper.js";
+import { CLINICAL_EXECUTE_API_PATH, CLINICAL_FOUR_ELEMENTS_PROOFREAD_APP_ID, CLINICAL_WORKFLOW_APP_TYPE, } from "../constants.js";
+import { fourElementsDraftToWorkflowInputs, parseFourElementsProofreadOutputs, validateFourElementsDraft, } from "../four-elements.js";
+import { buildClinicalWorkflowBody } from "../apps.js";
+import { streamClinicalWorkflow } from "../sse-utils.js";
+import { requireClinicalSession, updateClinicalSession, } from "../session-cache.js";
+export async function runPrecheckFourElements(options) {
+    const format = options.format ?? "markdown";
+    const session = await requireClinicalSession(options.sessionId);
+    const errors = validateFourElementsDraft(session.draft);
+    if (Object.keys(errors).length > 0) {
+        const result = {
+            status: "validation_failed",
+            nextAction: "fix_inputs",
+            errors,
+            firstErrorMessage: Object.values(errors)[0] ?? "",
+        };
+        if (format === "json") {
+            printOutput(wrapWorkbenchResult(result, { step: "four-elements-precheck", subType: "clinical" }, { sessionId: session.sessionId }), "json");
+        }
+        else {
+            const log = createFormatLogger(format);
+            log("\n四要素校验未通过：");
+            for (const message of Object.values(errors))
+                log(`- ${message}`);
+        }
+        return;
+    }
+    const inputs = fourElementsDraftToWorkflowInputs(session.draft);
+    const body = buildClinicalWorkflowBody({
+        appId: CLINICAL_FOUR_ELEMENTS_PROOFREAD_APP_ID,
+        appName: "四要素校对",
+        appType: CLINICAL_WORKFLOW_APP_TYPE,
+        inputs,
+    });
+    const stream = await streamClinicalWorkflow({
+        path: CLINICAL_EXECUTE_API_PATH,
+        body,
+        format,
+        startLabel: "正在预检四要素...",
+        progressLabel: "四要素预检中",
+        finishLabel: "四要素预检完成",
+        failureMessage: "四要素预检请求失败，请稍后重试",
+        emptyMessage: "四要素预检结果为空",
+        allowEmptyText: true,
+    });
+    const proofread = parseFourElementsProofreadOutputs(stream.outputs ?? {});
+    await updateClinicalSession(session, {
+        proofread,
+        precheckInputs: inputs,
+        article: undefined,
+    });
+    const success = proofread.outcome === "success";
+    const result = {
+        status: success ? "precheck_success" : "precheck_failed",
+        nextAction: success ? "generate_article" : "revise_four_elements",
+        outcome: proofread.outcome,
+        content: proofread.content,
+    };
+    if (format === "json") {
+        printOutput(wrapWorkbenchResult(result, { step: "four-elements-precheck", subType: "clinical" }, {
+            sessionId: session.sessionId,
+            workflowRunId: stream.workflowRunId,
+            cacheReady: true,
+        }), "json");
+        return;
+    }
+    const log = createFormatLogger(format);
+    log(success
+        ? "\n四要素预检成功，可以生成全文。\n"
+        : "\n四要素预检失败，请根据以下建议调整后重新预检。\n");
+    if (proofread.content)
+        log(`\n${proofread.content}\n`);
+}
+//# sourceMappingURL=four-elements-precheck.js.map

package/cli/dist/modules/fund/clinical/commands/four-elements-precheck.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/four-elements-update.d.ts

@@ -0,0 +1,16 @@
+import { type OutputFormat } from "../../../../core/index.js";
+interface BaseUpdateOptions {
+    sessionId?: string;
+    format?: OutputFormat;
+}
+export interface UpdateDesignOptions extends BaseUpdateOptions {
+    selectionsFile?: string;
+}
+export interface UpdateTextOptions extends BaseUpdateOptions {
+    file?: string;
+}
+export declare function runUpdateFourElementsDesign(options: UpdateDesignOptions): Promise<void>;
+export declare function runUpdateFourElementsPurpose(options: UpdateTextOptions): Promise<void>;
+export declare function runUpdateFourElementsOutcome(options: UpdateTextOptions): Promise<void>;
+export {};
+//# sourceMappingURL=four-elements-update.d.ts.map

package/cli/dist/modules/fund/clinical/commands/four-elements-update.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/four-elements-update.js

@@ -0,0 +1,108 @@
+import { createFormatLogger, helixlifeError, helixlifeErrorCode, printOutput, } from "../../../../core/index.js";
+import { wrapWorkbenchResult } from "../../../shared/result-wrapper.js";
+import { CLINICAL_EXECUTE_API_PATH, CLINICAL_PURPOSE_REGENERATE_APP_IDS, CLINICAL_WORKFLOW_APP_TYPE, } from "../constants.js";
+import { readClinicalStringMap, readClinicalTextFile, } from "../command-utils.js";
+import { applyDesignEditableFieldSelections, buildPurposeSyncInputs, canEditFourElementsDesign, patchOutcomeSampleFromOutputs, validateFourElementsText, } from "../four-elements.js";
+import { buildClinicalWorkflowBody } from "../apps.js";
+import { streamClinicalWorkflow } from "../sse-utils.js";
+import { invalidateClinicalPrecheck, requireClinicalSession, updateClinicalSession, } from "../session-cache.js";
+function printUpdated(result, sessionId, format, workflowRunId) {
+    if (format === "json") {
+        printOutput(wrapWorkbenchResult(result, { step: "four-elements", subType: "clinical" }, { sessionId, workflowRunId, cacheReady: true }), "json");
+    }
+}
+export async function runUpdateFourElementsDesign(options) {
+    const format = options.format ?? "markdown";
+    if (!options.selectionsFile) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "请通过 --selections-file 提供研究设计字段选择 JSON");
+    }
+    const session = await requireClinicalSession(options.sessionId);
+    const selections = await readClinicalStringMap(options.selectionsFile, "研究设计选择文件");
+    const draft = applyDesignEditableFieldSelections(session.draft, selections);
+    await updateClinicalSession(session, invalidateClinicalPrecheck(session, draft));
+    const result = {
+        status: "four_elements_updated",
+        nextAction: "review_or_precheck",
+        section: "design",
+        design: draft.design,
+        designEditableFields: draft.designEditableFields,
+        canEditDesign: canEditFourElementsDesign(draft),
+    };
+    printUpdated(result, session.sessionId, format);
+    if (format !== "json") {
+        createFormatLogger(format)(`\n## 研究设计\n\n${draft.design}\n`);
+    }
+}
+export async function runUpdateFourElementsPurpose(options) {
+    const format = options.format ?? "markdown";
+    if (!options.file) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "请通过 --file 提供研究目的 UTF-8 文件");
+    }
+    const session = await requireClinicalSession(options.sessionId);
+    const purpose = validateFourElementsText(await readClinicalTextFile(options.file, "研究目的文件"), "研究目的");
+    const editedDraft = { ...session.draft, purpose };
+    const appId = CLINICAL_PURPOSE_REGENERATE_APP_IDS[session.researchObjective];
+    const body = buildClinicalWorkflowBody({
+        appId,
+        appName: `${session.researchObjective}-重新生成结局指标及样本量计算`,
+        appType: CLINICAL_WORKFLOW_APP_TYPE,
+        inputs: buildPurposeSyncInputs(session.topicInputs, editedDraft),
+    });
+    const stream = await streamClinicalWorkflow({
+        path: CLINICAL_EXECUTE_API_PATH,
+        body,
+        format,
+        startLabel: "正在同步结局指标与样本量...",
+        progressLabel: "同步生成中",
+        finishLabel: "同步生成完成",
+        failureMessage: "结局指标与样本量同步失败，请稍后重试",
+        emptyMessage: "结局指标与样本量同步结果为空",
+        allowEmptyText: true,
+    });
+    const draft = patchOutcomeSampleFromOutputs(editedDraft, stream.outputs ?? {});
+    if (!draft.outcome.trim() || !draft.sample.trim()) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_RESPONSE, "研究目的已读取，但工作流未返回完整的结局指标和样本量");
+    }
+    await updateClinicalSession(session, invalidateClinicalPrecheck(session, draft));
+    const result = {
+        status: "four_elements_updated",
+        nextAction: "review_or_precheck",
+        section: "purpose",
+        purpose: draft.purpose,
+        outcome: draft.outcome,
+        sample: draft.sample,
+        designEditableFields: draft.designEditableFields,
+        canEditDesign: canEditFourElementsDesign(draft),
+    };
+    printUpdated(result, session.sessionId, format, stream.workflowRunId);
+    if (format !== "json") {
+        const log = createFormatLogger(format);
+        log(`\n## 研究目的\n\n${draft.purpose}`);
+        log(`\n## 结局指标\n\n${draft.outcome}`);
+        log(`\n## 样本量计算\n\n${draft.sample}\n`);
+    }
+}
+export async function runUpdateFourElementsOutcome(options) {
+    const format = options.format ?? "markdown";
+    if (!options.file) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "请通过 --file 提供结局指标 UTF-8 文件");
+    }
+    const session = await requireClinicalSession(options.sessionId);
+    const outcome = validateFourElementsText(await readClinicalTextFile(options.file, "结局指标文件"), "结局指标");
+    const draft = { ...session.draft, outcome };
+    await updateClinicalSession(session, invalidateClinicalPrecheck(session, draft));
+    const result = {
+        status: "four_elements_updated",
+        nextAction: "review_or_precheck",
+        section: "outcome",
+        outcome,
+        designEditableFields: draft.designEditableFields,
+        canEditDesign: canEditFourElementsDesign(draft),
+        warning: "修改结局指标后，请勿忘记同步检查研究目的",
+    };
+    printUpdated(result, session.sessionId, format);
+    if (format !== "json") {
+        createFormatLogger(format)(`\n## 结局指标\n\n${outcome}\n\n注意：请同步检查研究目的。\n`);
+    }
+}
+//# sourceMappingURL=four-elements-update.js.map

package/cli/dist/modules/fund/clinical/commands/four-elements-update.js.map

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

@@ -0,0 +1,14 @@
+import { type OutputFormat } from "../../../../core/index.js";
+export interface SampleSizeParametersOptions {
+    path?: string[];
+    format?: OutputFormat;
+}
+export interface CalculateSampleSizeOptions {
+    sessionId?: string;
+    path?: string[];
+    paramsFile?: string;
+    format?: OutputFormat;
+}
+export declare function runSampleSizeParameters(options: SampleSizeParametersOptions): Promise<void>;
+export declare function runCalculateSampleSize(options: CalculateSampleSizeOptions): Promise<void>;
+//# sourceMappingURL=sample-size.d.ts.map

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

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