helixlife-expert-cli 0.1.0

package/cli/dist/modules/fund/nsfc/parse-hypothesis.js

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+// 对齐前端 parse-nsfc-v2-* / parse-research-path-workflow-result
+/** 拼接候选基因的研究方向文案（directions 全量；无则 mechanism） */
+export function formatGeneResearchDirections(g) {
+    if (g.directions?.length) {
+        return g.directions.join("；");
+    }
+    const mechanism = String(g.mechanism ?? "").trim();
+    if (mechanism)
+        return mechanism;
+    return String(g.new_text || g.original_text || "").trim();
+}
+/**
+ * 缺失信息选项短标题：取括号前机制名（如 `ceRNA机制 (…)` → `ceRNA机制`）；
+ * 无括号则用全文。对齐「聊天展示全文 + 选择器短标题」。
+ */
+export function shortMissingInfoLabel(full) {
+    const text = String(full ?? "").trim();
+    const m = text.match(/^(.+?)\s*[（(]/);
+    return m ? m[1].trim() : text;
+}
+/**
+ * 构造候选基因选择器选项。
+ * UX：聊天先按基因列出研究方向全文；选择器 label 仅基因名（勿重复塞进 label）。
+ */
+export function buildGeneSelectionOptions(genes) {
+    return genes.map((g, i) => {
+        const gene = String(g.gene || g.id || "").trim() || `候选${i + 1}`;
+        const directions = formatGeneResearchDirections(g);
+        return {
+            index: i + 1,
+            label: gene,
+            description: directions
+                ? `研究方向：${directions}`
+                : "（暂无研究方向描述）",
+            value: gene,
+            mechanism: String(g.mechanism || g.original_text || "").trim(),
+            results: String(g.results ?? "").trim(),
+        };
+    });
+}
+/**
+ * 构造假说选择器选项。
+ * UX：聊天完整展示假说正文；选择器仅短标题（假说 N）。
+ */
+export function buildHypothesisSelectionOptions(hypotheses) {
+    const options = hypotheses.map((h, i) => {
+        const text = String(h.new_text || h.original_text || "").trim();
+        const n = i + 1;
+        return {
+            index: n,
+            label: `假说${["一", "二", "三", "四", "五", "六", "七", "八", "九", "十"][i] ?? String(n)}`,
+            description: text,
+            value: String(i),
+        };
+    });
+    options.push({
+        index: hypotheses.length + 1,
+        label: "自定义假说",
+        description: "由您自行提供假说内容",
+        value: "custom",
+    });
+    return options;
+}
+/**
+ * 构造缺失信息单块选择器选项。
+ * UX：聊天先列出选项全文（含括号说明）；选择器 label 仅短标题；
+ * value 仍为工作流全文，供 --picks-file 提交。
+ */
+export function buildMissingInfoBlockSelectionOptions(block) {
+    return block.select.map((opt, i) => {
+        const text = String(opt ?? "").trim();
+        return {
+            index: i + 1,
+            label: shortMissingInfoLabel(text),
+            description: text,
+            value: text,
+        };
+    });
+}
+const JSON_HYPO_KEY = /^json(\d+)$/i;
+const INFO_GENE_KEY = /^info_gene(\d+)$/i;
+function sortedKeys(obj, re) {
+    return Object.keys(obj)
+        .filter((k) => re.test(k))
+        .sort((a, b) => {
+        const na = Number(re.exec(a)?.[1] ?? 0);
+        const nb = Number(re.exec(b)?.[1] ?? 0);
+        return na - nb;
+    });
+}
+export function articleContentToJsonArrayString(raw) {
+    const normalized = String(raw ?? "").replace(/\r\n|\r|\n/g, "\r\n");
+    return JSON.stringify([normalized]);
+}
+export function splitGeneDirectionLines(direction) {
+    return String(direction ?? "")
+        .split(/\r\n|\r|\n/)
+        .map((s) => s.trim())
+        .filter(Boolean);
+}
+/** 解析假说列表 outputs.jsonN */
+export function parseNsfcV2HypothesisWorkflowResult(outputs) {
+    if (!outputs || typeof outputs !== "object")
+        return null;
+    const raw = outputs;
+    const keys = sortedKeys(raw, JSON_HYPO_KEY);
+    if (keys.length === 0)
+        return null;
+    const list = keys
+        .map((key, idx) => {
+        const block = raw[key];
+        const hypothesis = String(block?.hypothesis ?? "").trim();
+        if (!hypothesis)
+            return null;
+        return {
+            id: `hypothesis_${idx}`,
+            original_text: hypothesis,
+            new_text: hypothesis,
+        };
+    })
+        .filter((item) => item !== null);
+    return list.length > 0 ? list : null;
+}
+function isArticleWorkflowResult(result) {
+    if (!result || typeof result !== "object")
+        return false;
+    const r = result;
+    if (sortedKeys(r, INFO_GENE_KEY).length > 0)
+        return true;
+    const reportText = typeof r.report_text === "string" ? r.report_text.trim() : "";
+    if (reportText)
+        return true;
+    if (Array.isArray(r.info_dis) && r.info_dis.some((x) => String(x).trim())) {
+        return true;
+    }
+    if (Array.isArray(r.info_res) && r.info_res.some((x) => String(x).trim())) {
+        return true;
+    }
+    return false;
+}
+/** 解析文章分析 outputs.result → 背景 + 候选基因 */
+export function parseNsfcV2ArticleWorkflowResult(result) {
+    if (!isArticleWorkflowResult(result))
+        return null;
+    const r = result;
+    const reportText = typeof r.report_text === "string" ? r.report_text : "";
+    const keys = sortedKeys(r, INFO_GENE_KEY);
+    if (keys.length === 0) {
+        const reportTrim = reportText.trim();
+        const infoDisJoined = Array.isArray(r.info_dis)
+            ? r.info_dis
+                .map((x) => String(x).trim())
+                .filter(Boolean)
+                .join("\n\n")
+            : "";
+        const infoResJoined = Array.isArray(r.info_res)
+            ? r.info_res
+                .map((x) => String(x).trim())
+                .filter(Boolean)
+                .join("\n\n")
+            : "";
+        const background_report = [reportTrim, infoDisJoined, infoResJoined]
+            .filter(Boolean)
+            .join("\n\n\n");
+        if (!background_report)
+            return null;
+        return { backgroundReport: background_report, genes: [] };
+    }
+    const genes = keys.map((key, idx) => {
+        const info = r[key];
+        const gene = String(info?.gene ?? "").trim() || "候选";
+        const direction = String(info?.direction ?? "");
+        const lines = splitGeneDirectionLines(direction);
+        const preResult = String(info?.pre_result ?? "").trim();
+        const bodyText = lines.length > 0 ? lines.join("\n") : gene;
+        return {
+            id: `hypothesis_${idx}`,
+            original_text: bodyText,
+            new_text: bodyText,
+            gene,
+            directions: lines,
+            ...(direction ? { mechanism: direction } : {}),
+            ...(preResult ? { results: preResult } : {}),
+            ...(idx === 0 && reportText ? { background_report: reportText } : {}),
+        };
+    });
+    return {
+        backgroundReport: reportText,
+        genes,
+    };
+}
+export function buildNsfcV2GenePreResultsText(genes) {
+    if (!Array.isArray(genes) || genes.length === 0)
+        return "";
+    return genes
+        .map((item) => String(item?.results ?? "").trim())
+        .filter(Boolean)
+        .join("\n\n");
+}
+export function getResearchPathReportText(result) {
+    if (!result || typeof result !== "object")
+        return "";
+    const part1 = result.PART1;
+    if (part1 && typeof part1 === "object" && !Array.isArray(part1)) {
+        const c = part1.content;
+        if (typeof c === "string" && c.trim())
+            return c.trim();
+    }
+    const rt = result.report_text;
+    if (typeof rt === "string" && rt.trim())
+        return rt.trim();
+    return "";
+}
+function dedupeSelect(items) {
+    const seen = new Set();
+    const out = [];
+    for (const s of items) {
+        if (!seen.has(s)) {
+            seen.add(s);
+            out.push(s);
+        }
+    }
+    return out;
+}
+export function parseMissingInfoFromAnalysisResult(result) {
+    if (!result || typeof result !== "object")
+        return [];
+    const part2 = result.PART2;
+    if (!part2 || typeof part2 !== "object")
+        return [];
+    const blocks = [];
+    for (const section of Object.values(part2)) {
+        if (!section || typeof section !== "object" || Array.isArray(section)) {
+            continue;
+        }
+        const v = section;
+        for (const [k, val] of Object.entries(v)) {
+            const kl = k.toLowerCase();
+            if (!kl.includes("thirdheading") || !kl.includes("title"))
+                continue;
+            const title = typeof val === "string" ? val : "";
+            const selectKey = k.replace(/title/i, "select");
+            const raw = v[selectKey];
+            const select = raw && typeof raw === "object" && !Array.isArray(raw)
+                ? Object.values(raw).filter((x) => typeof x === "string" && String(x).trim())
+                : [];
+            blocks.push({ title, select: dedupeSelect(select) });
+        }
+    }
+    return blocks;
+}
+export function isMissingInfoCustomOption(optionLabel) {
+    return optionLabel.includes("自定义");
+}
+/** 从 outputs 统一尝试解析假说列表 */
+export function tryParseHypothesisList(outputs) {
+    if (!outputs)
+        return [];
+    const fromResult = parseNsfcV2ArticleWorkflowResult(outputs.result);
+    if (fromResult?.genes.length) {
+        return fromResult.genes;
+    }
+    const fromJson = parseNsfcV2HypothesisWorkflowResult(outputs);
+    if (fromJson?.length)
+        return fromJson;
+    const text = outputs.text;
+    if (typeof text === "string" && text.trim()) {
+        return [
+            {
+                id: "hypothesis_0",
+                original_text: text.trim(),
+                new_text: text.trim(),
+            },
+        ];
+    }
+    return [];
+}
+//# sourceMappingURL=parse-hypothesis.js.map

package/cli/dist/modules/fund/nsfc/parse-hypothesis.js.map

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package/cli/dist/modules/fund/nsfc/parse-outline.d.ts

@@ -0,0 +1,23 @@
+export declare function extractOutlineBlocks(markdown: string): Record<string, string>;
+/** Step4 全文工作流入参：inputs.input JSON 字符串 */
+export declare function stringifyNsfcOutlineWorkflowInput(markdown: string, hypothesis: string, isNsfcV2?: boolean): string;
+/** 轻量校验：至少含一个二级标题 */
+export declare function assertOutlineHasH2(markdown: string): void;
+/** 从 session outlineParams / inputs 组装提纲工作流 slim body */
+export declare function buildNsfcOutlineSlimBody(session: {
+    confirmedHypothesis?: string;
+    outlineParams?: {
+        query: string;
+        inputs: Record<string, unknown>;
+    };
+    genePreResultsText?: string;
+    inputs: Record<string, unknown>;
+}): {
+    query: string;
+    inputs: {
+        program: string;
+        text: string;
+        results: string;
+    };
+};
+//# sourceMappingURL=parse-outline.d.ts.map

package/cli/dist/modules/fund/nsfc/parse-outline.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"parse-outline.d.ts","sourceRoot":"","sources":["../../../../src/modules/fund/nsfc/parse-outline.ts"],"names":[],"mappings":"AAQA,wBAAgB,oBAAoB,CAClC,QAAQ,EAAE,MAAM,GACf,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CA6CxB;AAED,0CAA0C;AAC1C,wBAAgB,iCAAiC,CAC/C,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAClB,QAAQ,UAAO,GACd,MAAM,CAYR;AAED,qBAAqB;AACrB,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,CAOzD;AAED,yDAAyD;AACzD,wBAAgB,wBAAwB,CAAC,OAAO,EAAE;IAChD,mBAAmB,CAAC,EAAE,MAAM,CAAC;IAC7B,aAAa,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAA;KAAE,CAAC;IACnE,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CACjC,GAAG;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CA8BhF"}

package/cli/dist/modules/fund/nsfc/parse-outline.js

@@ -0,0 +1,91 @@
+// 国自然提纲 Markdown 解析 / 全文入参序列化（对齐前端 outline.ts）
+const OUTLINE_BLOCKS = {
+    pp_outline: "## 立项提纲",
+    proposed: "## 为了验证以上科学假设，本项目拟开展以下研究内容：",
+    res_content: "## 研究内容",
+};
+export function extractOutlineBlocks(markdown) {
+    const result = {};
+    const lines = markdown.split("\n");
+    const sectionInfo = [];
+    for (let i = 0; i < lines.length; i++) {
+        const line = lines[i].trim();
+        if (line.startsWith("## ") && !line.startsWith("###")) {
+            const title = line.replace(/^##\s+/, "").trim();
+            sectionInfo.push({
+                title,
+                startIndex: i,
+                endIndex: lines.length - 1,
+            });
+        }
+    }
+    for (let i = 0; i < sectionInfo.length; i++) {
+        if (i < sectionInfo.length - 1) {
+            sectionInfo[i].endIndex = sectionInfo[i + 1].startIndex - 1;
+        }
+    }
+    for (const [key, identifier] of Object.entries(OUTLINE_BLOCKS)) {
+        const targetTitle = identifier.replace(/^##\s+/, "").trim();
+        const matched = sectionInfo.find((s) => s.title === targetTitle);
+        if (!matched) {
+            result[key] = "";
+            continue;
+        }
+        let content = lines[matched.startIndex];
+        for (let i = matched.startIndex + 1; i <= matched.endIndex; i++) {
+            if (lines[i].trim() !== "" ||
+                (i > matched.startIndex + 1 && lines[i - 1].trim() !== "")) {
+                content += "\n" + lines[i];
+            }
+        }
+        result[key] = content.trim();
+    }
+    return result;
+}
+/** Step4 全文工作流入参：inputs.input JSON 字符串 */
+export function stringifyNsfcOutlineWorkflowInput(markdown, hypothesis, isNsfcV2 = true) {
+    if (isNsfcV2) {
+        return JSON.stringify({
+            output: markdown ?? "",
+            ...extractOutlineBlocks(markdown),
+            hypothesis: hypothesis ?? "",
+        });
+    }
+    return JSON.stringify({
+        ...extractOutlineBlocks(markdown),
+        hypothesis: hypothesis ?? "",
+    });
+}
+/** 轻量校验：至少含一个二级标题 */
+export function assertOutlineHasH2(markdown) {
+    const ok = /^##\s+\S+/m.test(markdown.trim());
+    if (!ok) {
+        throw new Error("提纲 Markdown 须至少包含一个二级标题（## …），以符合生成全文格式");
+    }
+}
+/** 从 session outlineParams / inputs 组装提纲工作流 slim body */
+export function buildNsfcOutlineSlimBody(session) {
+    const op = session.outlineParams;
+    const query = String(op?.query ??
+        session.confirmedHypothesis ??
+        session.inputs.text ??
+        "").trim();
+    const src = op?.inputs ?? session.inputs;
+    const projectLevel = String(src.projectLevel ?? session.inputs.projectLevel ?? "");
+    const isProvince = projectLevel === "省部级";
+    const program = isProvince
+        ? "省市级别项目"
+        : String(src.program ?? src.project ?? "");
+    const text = String(src.text ?? query).trim() || query;
+    const parsedAttachment = String(session.genePreResultsText ?? src.gene_pre_results_text ?? "").trim();
+    const fallbackResults = String(src.results ?? "");
+    return {
+        query,
+        inputs: {
+            program,
+            text,
+            results: parsedAttachment || fallbackResults,
+        },
+    };
+}
+//# sourceMappingURL=parse-outline.js.map

package/cli/dist/modules/fund/nsfc/parse-outline.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/nsfc/png-watermark.d.ts

@@ -0,0 +1,24 @@
+/** 与原站 tech-roadmap / hypothesis-figure 一致 */
+export declare const NSFC_IMAGE_CONTENT_PRODUCER = "Helix";
+export interface ApplyPngWatermarkOptions {
+    pngBuffer: Buffer;
+    produceId?: string;
+    /** 假说机制图用白色底；技术路线图默认透明留白 */
+    paddingColor?: string;
+}
+export interface ApplyPngWatermarkResult {
+    buffer: Buffer;
+    watermarked: boolean;
+    error?: string;
+}
+/**
+ * 底部追加留白（对齐原站 addBottomPaddingToImage，默认 60px）。
+ * 用 base64 data URI 内嵌原图——resvg-js 不会加载 file:// 外链，
+ * 用外链会丢失原图内容导致空白（已踩坑）。
+ */
+export declare function addBottomPaddingToPng(pngBuffer: Buffer, paddingHeight?: number, paddingColor?: string): Buffer;
+/**
+ * 打「AI生成」水印；接口失败时降级返回原图（与原站一致）。
+ */
+export declare function applyPngWatermark(options: ApplyPngWatermarkOptions): Promise<ApplyPngWatermarkResult>;
+//# sourceMappingURL=png-watermark.d.ts.map

package/cli/dist/modules/fund/nsfc/png-watermark.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/nsfc/png-watermark.js

@@ -0,0 +1,78 @@
+/**
+ * PNG 水印：底部留白 + PaaS png/to/png（对齐原站 addLabelToImage）
+ * 失败时降级返回原图。
+ */
+import { Resvg } from "@resvg/resvg-js";
+import { ApiClient, getDefaultNewideaBaseUrl, } from "../../../core/index.js";
+/** 与原站 tech-roadmap / hypothesis-figure 一致 */
+export const NSFC_IMAGE_CONTENT_PRODUCER = "Helix";
+const BOTTOM_PADDING_PX = 60;
+/** 从 PNG IHDR 读取宽高 */
+function readPngSize(png) {
+    if (png.length < 24 || png[0] !== 0x89 || png[1] !== 0x50) {
+        throw new Error("invalid PNG");
+    }
+    return {
+        width: png.readUInt32BE(16),
+        height: png.readUInt32BE(20),
+    };
+}
+/**
+ * 底部追加留白（对齐原站 addBottomPaddingToImage，默认 60px）。
+ * 用 base64 data URI 内嵌原图——resvg-js 不会加载 file:// 外链，
+ * 用外链会丢失原图内容导致空白（已踩坑）。
+ */
+export function addBottomPaddingToPng(pngBuffer, paddingHeight = BOTTOM_PADDING_PX, paddingColor) {
+    const { width, height } = readPngSize(pngBuffer);
+    const href = `data:image/png;base64,${pngBuffer.toString("base64")}`;
+    const padFill = paddingColor
+        ? `<rect x="0" y="${height}" width="${width}" height="${paddingHeight}" fill="${paddingColor}"/>`
+        : "";
+    const svg = `<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" width="${width}" height="${height + paddingHeight}">
+  <image x="0" y="0" width="${width}" height="${height}" href="${href}"/>
+  ${padFill}
+</svg>`;
+    return Buffer.from(new Resvg(svg).render().asPng());
+}
+async function callPngToPng(pngBuffer, produceId) {
+    const form = new FormData();
+    form.append("data", new Blob([new Uint8Array(pngBuffer)], { type: "image/png" }), "image.png");
+    form.append("is_aigc", "true");
+    form.append("content_producer", NSFC_IMAGE_CONTENT_PRODUCER);
+    form.append("produce_id", produceId || "");
+    const client = new ApiClient();
+    const { buffer } = await client.requestBinary("data_conversion/v2/png/to/png", {
+        method: "POST",
+        baseUrl: getDefaultNewideaBaseUrl(),
+        body: form,
+    });
+    return buffer;
+}
+/**
+ * 打「AI生成」水印；接口失败时降级返回原图（与原站一致）。
+ */
+export async function applyPngWatermark(options) {
+    const { pngBuffer, produceId = "", paddingColor } = options;
+    try {
+        const padded = addBottomPaddingToPng(pngBuffer, BOTTOM_PADDING_PX, paddingColor);
+        const watermarked = await callPngToPng(padded, produceId);
+        if (!watermarked.length) {
+            return {
+                buffer: pngBuffer,
+                watermarked: false,
+                error: "png/to/png 返回空内容",
+            };
+        }
+        return { buffer: watermarked, watermarked: true };
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        return {
+            buffer: pngBuffer,
+            watermarked: false,
+            error: message.slice(0, 300),
+        };
+    }
+}
+//# sourceMappingURL=png-watermark.js.map

package/cli/dist/modules/fund/nsfc/png-watermark.js.map

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package/cli/dist/modules/fund/nsfc/prompt-hypothesis.d.ts

@@ -0,0 +1,20 @@
+import { type NsfcHasHypothesis, type NsfcPriorResult, type NsfcProjectLevel, type NsfcProjectType } from "./constants.js";
+export interface NsfcHypothesisPromptResult {
+    hasHypothesis: NsfcHasHypothesis;
+    projectLevel: NsfcProjectLevel;
+    project?: NsfcProjectType;
+    priorResult?: NsfcPriorResult;
+    query: string;
+    disease?: string;
+    attachPath?: string;
+}
+export declare function promptNsfcHypothesisCreate(partial: {
+    hasHypothesis?: NsfcHasHypothesis;
+    projectLevel?: NsfcProjectLevel;
+    project?: NsfcProjectType;
+    priorResult?: NsfcPriorResult;
+    query?: string;
+    disease?: string;
+    attachPath?: string;
+}): Promise<NsfcHypothesisPromptResult>;
+//# sourceMappingURL=prompt-hypothesis.d.ts.map

package/cli/dist/modules/fund/nsfc/prompt-hypothesis.d.ts.map

@@ -0,0 +1 @@
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