@seqyuan/annodex 0.1.12 → 0.1.13

package/lib/report-store.ts

@@ -1,597 +0,0 @@
-import { existsSync, mkdirSync, readFileSync, renameSync, writeFileSync } from "fs";
-import { dirname, join } from "path";
-import type { AgentMessage, SessionContext } from "@/lib/types";
-
-// ---- Local getConfigDir (annodex config) ----
-function getAgentDir(): string {
-  const homeDir = process.env.HOME ?? process.env.USERPROFILE ?? "/tmp";
-  return join(homeDir, ".config", "annodex");
-}
-
-export interface AnalysisReportSource {
-  type: "session" | "file";
-  id?: string;
-  path?: string;
-  label: string;
-}
-
-export interface AnalysisReportChange {
-  id: string;
-  timestamp: string;
-  title: string;
-  detail: string;
-}
-
-export interface AnalysisReportSection {
-  id: string;
-  title: string;
-  markdown: string;
-  status: "draft" | "verified" | "outdated" | "needs_review";
-  updatedAt: string | null;
-  sources: AnalysisReportSource[];
-}
-
-export interface AnalysisReport {
-  schemaVersion: 1;
-  sessionId: string;
-  cwd: string;
-  title: string;
-  createdAt: string;
-  updatedAt: string;
-  markdown: string;
-  sections: AnalysisReportSection[];
-  sources: AnalysisReportSource[];
-  changes: AnalysisReportChange[];
-  appliedUpdateKeys?: string[];
-}
-
-export interface AnalysisReportUpdate {
-  topic?: string;
-  section?: string;
-  action?: "append" | "replace";
-  status?: AnalysisReportSection["status"];
-  markdown?: string;
-  sources?: Array<string | AnalysisReportSource>;
-  invalidates?: string[];
-  note?: string;
-}
-
-const SECTION_DEFS = [
-  { id: "objective", title: "Objective" },
-  { id: "input_data", title: "Input Data" },
-  { id: "methods", title: "Methods" },
-  { id: "quality_control", title: "Quality Control" },
-  { id: "results", title: "Results" },
-  { id: "interpretation", title: "Biological Interpretation" },
-  { id: "outputs", title: "Output Files" },
-  { id: "reproducibility", title: "Reproducibility" },
-] as const;
-
-const FILE_PATH_RE = /(?:^|[\s(["'`])((?:\.{1,2}\/|\/|~\/)?[A-Za-z0-9_.@+\-/\\]+?\.(?:csv|tsv|txt|xlsx|xls|pdf|png|jpg|jpeg|svg|html|htm|r|R|py|ipynb|qmd|md|rds|h5ad|loom|mtx|tsv\.gz|csv\.gz))(?:$|[\s)\]"'`,;:])/g;
-const OUTPUT_DIR_RE = /(?:^|[\s(["'`])((?:\.{1,2}\/|\/|~\/)?[A-Za-z0-9_.@+\-/\\]+\/)(?=\s*(?:[:：-]|[0-9]+|含|共|files?|个文件|PDFs?|PNGs?|CSVs?|TSVs?|输出|output|results?))/gim;
-const METHOD_RE = /\b(seurat|scanpy|single[- ]cell|scrna|qc|quality control|normalize|normalization|pca|umap|tsne|cluster|clustering|resolution|marker|differential expression|deg|go enrichment|kegg|reactome|pathway|cell type|annotation|doublet|batch|integration|harmony|scvi)\b/i;
-const RESULT_RE = /\b(result|found|identified|showed|observed|enriched|upregulated|downregulated|marker|cluster|cell type|figure|plot|table|significant|p\s*[<>=]|fdr|padj|logfc|auc)\b/i;
-const INTERPRET_RE = /\b(suggest|indicate|imply|consistent with|biological|interpret|likely|may reflect|supports|driven by|associated with)\b/i;
-const QC_RE = /\b(qc|quality control|filter|filtered|mitochondrial|percent\.mt|nfeature|ncount|doublet|ambient|low[- ]quality)\b/i;
-const BIO_ANALYSIS_RE = /\b(seurat|scanpy|single[- ]cell|scrna|sc[- ]rna|rna[- ]seq|transcriptom|gene|genes|marker|cell type|cluster|clustering|umap|tsne|pca|qc|mitochondrial|percent\.mt|nfeature|ncount|deg|differential expression|go enrichment|kegg|reactome|pathway|gsea|volcano|heatmap|h5ad|rds|loom|mtx|fastq|bam|vcf|counts?|expression|annotation|doublet|batch|integration|harmony|scvi)\b|生信|单细胞|转录组|基因|表达矩阵|差异表达|富集|通路|聚类|细胞类型|细胞注释|质控|线粒体|标记基因|火山图|热图/i;
-const EMPTY_SECTION_MARKDOWN = new Set([
-  "_No curated content yet._",
-  "_No analysis objective detected yet._",
-  "_No input data paths detected yet._",
-  "_No output files detected yet._",
-  "_No reproducibility notes detected yet._",
-]);
-
-function nowIso(): string {
-  return new Date().toISOString();
-}
-
-function encodePathSegment(value: string): string {
-  return Buffer.from(value).toString("base64url");
-}
-
-export function getReportPath(sessionId: string): string {
-  return join(getAgentDir(), "reports", `${encodePathSegment(sessionId)}.json`);
-}
-
-function makeEmptySection(id: string, title: string): AnalysisReportSection {
-  return { id, title, markdown: "", status: "draft", updatedAt: null, sources: [] };
-}
-
-function normalizeEmptyMarkdown(value: string): string {
-  const trimmed = value.trim();
-  return EMPTY_SECTION_MARKDOWN.has(trimmed) ? "" : trimmed;
-}
-
-function hasReportSectionContent(sections: AnalysisReportSection[]): boolean {
-  return sections.some((section) => normalizeEmptyMarkdown(section.markdown).length > 0);
-}
-
-export function createEmptyReport(sessionId: string, cwd: string, title?: string): AnalysisReport {
-  const timestamp = nowIso();
-  const sections = SECTION_DEFS.map((section) => makeEmptySection(section.id, section.title));
-  return {
-    schemaVersion: 1,
-    sessionId,
-    cwd,
-    title: title || "Analysis Report",
-    createdAt: timestamp,
-    updatedAt: timestamp,
-    markdown: "",
-    sections,
-    sources: [],
-    changes: [],
-    appliedUpdateKeys: [],
-  };
-}
-
-export function readReport(sessionId: string, cwd = "", title?: string): AnalysisReport {
-  const filePath = getReportPath(sessionId);
-  if (!existsSync(filePath)) return createEmptyReport(sessionId, cwd, title);
-
-  try {
-    const parsed = JSON.parse(readFileSync(filePath, "utf8")) as Partial<AnalysisReport>;
-    const fallback = createEmptyReport(sessionId, cwd, title);
-    const existingSections = Array.isArray(parsed.sections) ? parsed.sections : [];
-    const sections = SECTION_DEFS.map((def) => {
-      const existing = existingSections.find((section) => section?.id === def.id);
-      const markdown = normalizeEmptyMarkdown(typeof existing?.markdown === "string" ? existing.markdown : "");
-      return {
-        ...makeEmptySection(def.id, def.title),
-        ...(existing && typeof existing === "object" ? existing : {}),
-        id: def.id,
-        title: def.title,
-        markdown,
-        status: markdown ? (existing?.status ?? "draft") : "draft",
-        updatedAt: markdown ? (existing?.updatedAt ?? null) : null,
-        sources: markdown && Array.isArray(existing?.sources) ? existing.sources : [],
-      };
-    });
-    const reportTitle = typeof parsed.title === "string" && parsed.title.trim() ? parsed.title : fallback.title;
-    return {
-      ...fallback,
-      ...parsed,
-      schemaVersion: 1,
-      sessionId,
-      cwd: typeof parsed.cwd === "string" ? parsed.cwd : cwd,
-      title: reportTitle,
-      createdAt: typeof parsed.createdAt === "string" ? parsed.createdAt : fallback.createdAt,
-      updatedAt: typeof parsed.updatedAt === "string" ? parsed.updatedAt : fallback.updatedAt,
-      sections,
-      markdown: renderReportMarkdown(reportTitle, sections),
-      sources: hasReportSectionContent(sections) && Array.isArray(parsed.sources) ? parsed.sources : [],
-      changes: hasReportSectionContent(sections) && Array.isArray(parsed.changes) ? parsed.changes : [],
-      appliedUpdateKeys: Array.isArray(parsed.appliedUpdateKeys)
-        ? parsed.appliedUpdateKeys.filter((key): key is string => typeof key === "string")
-        : [],
-    };
-  } catch {
-    return createEmptyReport(sessionId, cwd, title);
-  }
-}
-
-function stableHash(value: string): string {
-  let hash = 2166136261;
-  for (let i = 0; i < value.length; i++) {
-    hash ^= value.charCodeAt(i);
-    hash = Math.imul(hash, 16777619);
-  }
-  return (hash >>> 0).toString(36);
-}
-
-export function writeReport(report: AnalysisReport): AnalysisReport {
-  const timestamp = nowIso();
-  const next = {
-    ...report,
-    updatedAt: timestamp,
-    markdown: renderReportMarkdown(report.title, report.sections),
-  };
-  const filePath = getReportPath(report.sessionId);
-  mkdirSync(dirname(filePath), { recursive: true });
-  const tempPath = `${filePath}.tmp`;
-  writeFileSync(tempPath, JSON.stringify(next, null, 2), "utf8");
-  renameSync(tempPath, filePath);
-  return next;
-}
-
-function cleanText(value: string): string {
-  return value.replace(/\s+/g, " ").trim();
-}
-
-function escapeMarkdown(value: string): string {
-  return value.replace(/\|/g, "\\|");
-}
-
-function outputKind(filePath: string): string {
-  const lower = filePath.toLowerCase();
-  if (/\.(png|jpe?g|svg)$/.test(lower)) return "Representative image/figure.";
-  if (/\.pdf$/.test(lower)) return "PDF figure or report.";
-  if (/\.(csv|tsv|csv\.gz|tsv\.gz|xlsx?|mtx)$/.test(lower)) return "Result table or matrix.";
-  if (/\.(r|py|ipynb|qmd|md)$/.test(lower)) return "Analysis script or document.";
-  if (/\.(rds|h5ad|loom)$/.test(lower)) return "Analysis object or dataset.";
-  if (/\.(html?|svg)$/.test(lower)) return "Browser-renderable output.";
-  return "Detected from session output.";
-}
-
-function isReportPreviewImage(filePath: string): boolean {
-  return /\.(png|jpe?g|svg)$/i.test(filePath);
-}
-
-function markdownImagePath(filePath: string): string {
-  return filePath.replace(/\\/g, "/").replace(/([()\s])/g, "\\$1");
-}
-
-function outputLabel(filePath: string): string {
-  return filePath.split(/[\\/]/).filter(Boolean).pop() ?? filePath;
-}
-
-function normalizeTopic(value?: string): string {
-  return cleanText(value ?? "").slice(0, 120);
-}
-
-function withTopicPrefix(markdown: string, topic?: string): string {
-  const trimmed = markdown.trim();
-  if (!trimmed) return "";
-  const normalizedTopic = normalizeTopic(topic);
-  if (!normalizedTopic) return trimmed;
-  const topicHeading = `### ${normalizedTopic}`;
-  if (trimmed === topicHeading || trimmed.startsWith(`${topicHeading}\n`)) return trimmed;
-  return `${topicHeading}\n\n${trimmed}`;
-}
-
-function messageText(message: AgentMessage): string {
-  const content = message.content;
-  if (typeof content === "string") return cleanText(content);
-  if (!Array.isArray(content)) return "";
-  return cleanText(content
-    .map((block) => {
-      if (block.type === "text") return block.text;
-      if (block.type === "toolCall") return `${block.toolName} ${JSON.stringify(block.input)}`;
-      return "";
-    })
-    .join(" "));
-}
-
-function firstUserText(context: SessionContext): string {
-  const first = context.messages.find((message) => message.role === "user");
-  return first ? messageText(first).slice(0, 900) : "";
-}
-
-function firstAnalysisUserText(context: SessionContext): string {
-  const first = context.messages.find((message) => message.role === "user" && BIO_ANALYSIS_RE.test(messageText(message)));
-  return first ? messageText(first).slice(0, 900) : "";
-}
-
-function sessionHasBioAnalysisContent(context: SessionContext): boolean {
-  return context.messages.some((message) => BIO_ANALYSIS_RE.test(messageText(message)));
-}
-
-function uniquePush(values: string[], value: string, max: number): void {
-  const cleaned = cleanText(value);
-  if (!cleaned || values.includes(cleaned)) return;
-  values.push(cleaned);
-  if (values.length > max) values.length = max;
-}
-
-function extractOutputFiles(context: SessionContext): string[] {
-  const files: string[] = [];
-  for (const message of context.messages) {
-    const text = messageText(message);
-    if (!text) continue;
-    for (const match of text.matchAll(FILE_PATH_RE)) {
-      const filePath = match[1]?.replace(/[.,;:)]+$/, "");
-      if (filePath) uniquePush(files, filePath, 30);
-    }
-    for (const match of text.matchAll(OUTPUT_DIR_RE)) {
-      const dirPath = match[1]?.replace(/[.,;:)]+$/, "");
-      if (dirPath) uniquePush(files, dirPath, 30);
-    }
-  }
-  return files;
-}
-
-function collectSessionSignals(context: SessionContext): {
-  methods: string[];
-  qc: string[];
-  results: string[];
-  interpretation: string[];
-  reproducibility: string[];
-} {
-  const methods: string[] = [];
-  const qc: string[] = [];
-  const results: string[] = [];
-  const interpretation: string[] = [];
-  const reproducibility: string[] = [];
-
-  for (const message of context.messages) {
-    const text = messageText(message);
-    if (!text || text.length < 12) continue;
-    const trimmed = text.length > 500 ? `${text.slice(0, 500).trim()}...` : text;
-
-    if (message.role === "assistant") {
-      if (QC_RE.test(trimmed)) uniquePush(qc, trimmed, 8);
-      if (METHOD_RE.test(trimmed)) uniquePush(methods, trimmed, 10);
-      if (RESULT_RE.test(trimmed)) uniquePush(results, trimmed, 12);
-      if (INTERPRET_RE.test(trimmed)) uniquePush(interpretation, trimmed, 8);
-    }
-
-    if (message.role === "toolResult" && /saved|wrote|created|exported|generated|output|success/i.test(trimmed)) {
-      uniquePush(reproducibility, trimmed, 8);
-    }
-  }
-
-  return { methods, qc, results, interpretation, reproducibility };
-}
-
-function bullets(items: string[], empty = "_No curated content yet._"): string {
-  if (items.length === 0) return empty;
-  return items.map((item) => `- ${item}`).join("\n");
-}
-
-function outputTable(files: string[]): string {
-  if (files.length === 0) return "";
-  return [
-    "| File or Directory | Notes |",
-    "| --- | --- |",
-    ...files.map((file) => `| \`${escapeMarkdown(file)}\` | ${outputKind(file)} |`),
-  ].join("\n");
-}
-
-function representativeFigures(files: string[], maxFigures = 4): string {
-  const figures = files.filter(isReportPreviewImage).slice(0, maxFigures);
-  if (figures.length === 0) return "";
-  return [
-    "#### Representative Figures",
-    "",
-    ...figures.flatMap((file) => {
-      const label = outputLabel(file);
-      return [
-        `![${label}](${markdownImagePath(file)})`,
-        "",
-        `_Figure: ${label}. Representative visual output detected from this analysis topic._`,
-        "",
-      ];
-    }),
-  ].join("\n").trim();
-}
-
-function combineMarkdown(parts: string[]): string {
-  return parts.map((part) => part.trim()).filter(Boolean).join("\n\n");
-}
-
-function updateSection(
-  report: AnalysisReport,
-  id: string,
-  markdown: string,
-  status: AnalysisReportSection["status"] = "draft",
-  sources: AnalysisReportSource[] = []
-): void {
-  const section = report.sections.find((item) => item.id === id);
-  if (!section) return;
-  section.markdown = markdown.trim();
-  section.status = status;
-  section.updatedAt = nowIso();
-  section.sources = sources;
-}
-
-function normalizeSectionId(section?: string): string | null {
-  if (!section) return null;
-  const normalized = section.trim().toLowerCase().replace(/[^a-z0-9]+/g, "_").replace(/^_+|_+$/g, "");
-  if (SECTION_DEFS.some((def) => def.id === normalized)) return normalized;
-  if (normalized.includes("objective") || normalized.includes("goal")) return "objective";
-  if (normalized.includes("input") || normalized.includes("sample") || normalized.includes("data")) return "input_data";
-  if (normalized.includes("method") || normalized.includes("parameter") || normalized.includes("workflow")) return "methods";
-  if (normalized.includes("qc") || normalized.includes("quality") || normalized.includes("filter")) return "quality_control";
-  if (normalized.includes("result") || normalized.includes("marker") || normalized.includes("deg") || normalized.includes("enrichment")) return "results";
-  if (normalized.includes("interpret") || normalized.includes("biology") || normalized.includes("biological")) return "interpretation";
-  if (normalized.includes("output") || normalized.includes("file") || normalized.includes("figure")) return "outputs";
-  if (normalized.includes("reproduc")) return "reproducibility";
-  return null;
-}
-
-function normalizeSources(sources: AnalysisReportUpdate["sources"]): AnalysisReportSource[] {
-  if (!Array.isArray(sources)) return [];
-  const normalized: AnalysisReportSource[] = [];
-  for (const source of sources) {
-    if (typeof source === "string") {
-      normalized.push({ type: "file", path: source, label: source });
-    } else if (source && typeof source === "object" && typeof source.label === "string") {
-      normalized.push({
-        type: source.type === "session" ? "session" : "file",
-        id: typeof source.id === "string" ? source.id : undefined,
-        path: typeof source.path === "string" ? source.path : undefined,
-        label: source.label,
-      });
-    }
-  }
-  return normalized;
-}
-
-export function applyReportUpdate(report: AnalysisReport, update: AnalysisReportUpdate, updateKey?: string): AnalysisReport {
-  const sectionId = normalizeSectionId(update.section);
-  const markdown = typeof update.markdown === "string" ? withTopicPrefix(update.markdown, update.topic) : "";
-  if (!sectionId || !markdown) return report;
-  const dedupeKey = updateKey ? stableHash(updateKey) : null;
-  if (dedupeKey && report.appliedUpdateKeys?.includes(dedupeKey)) return report;
-
-  const timestamp = nowIso();
-  const next: AnalysisReport = {
-    ...report,
-    sections: report.sections.map((section) => ({ ...section, sources: [...section.sources] })),
-    sources: [...report.sources],
-    changes: [...report.changes],
-    appliedUpdateKeys: [...(report.appliedUpdateKeys ?? [])],
-  };
-  const section = next.sections.find((item) => item.id === sectionId);
-  if (!section) return report;
-
-  section.markdown = update.action === "replace" || !section.markdown.trim()
-    ? markdown
-    : `${section.markdown.trim()}\n\n${markdown}`;
-  section.status = update.status ?? "draft";
-  section.updatedAt = timestamp;
-  const sources = normalizeSources(update.sources);
-  section.sources = sources.length > 0 ? sources : section.sources;
-
-  const invalidates = Array.isArray(update.invalidates) ? update.invalidates.map(normalizeSectionId).filter(Boolean) : [];
-  for (const invalidated of invalidates) {
-    const invalidatedSection = next.sections.find((item) => item.id === invalidated);
-    if (invalidatedSection && invalidatedSection.id !== section.id) {
-      invalidatedSection.status = "outdated";
-      invalidatedSection.updatedAt = timestamp;
-    }
-  }
-
-  next.sources = [...next.sources, ...sources].filter((source, index, all) => {
-    const key = `${source.type}:${source.id ?? ""}:${source.path ?? ""}:${source.label}`;
-    return all.findIndex((candidate) => `${candidate.type}:${candidate.id ?? ""}:${candidate.path ?? ""}:${candidate.label}` === key) === index;
-  });
-  next.changes = [
-    {
-      id: `change-${Date.now()}`,
-      timestamp,
-      title: `Updated ${section.title}`,
-      detail: update.note || "Applied a structured analysis report update from the assistant.",
-    },
-    ...next.changes,
-  ].slice(0, 50);
-  if (dedupeKey) {
-    next.appliedUpdateKeys = [dedupeKey, ...(next.appliedUpdateKeys ?? [])].slice(0, 500);
-  }
-  return next;
-}
-
-export function generateReportFromSession(input: {
-  report: AnalysisReport;
-  context: SessionContext;
-  sessionTitle?: string;
-  topic?: string;
-}): AnalysisReport {
-  const report = {
-    ...input.report,
-    title: input.report.title || input.sessionTitle || "Analysis Report",
-    sections: input.report.sections.map((section) => ({ ...section, sources: [...section.sources] })),
-    sources: [...input.report.sources],
-    changes: [...input.report.changes],
-    appliedUpdateKeys: [...(input.report.appliedUpdateKeys ?? [])],
-  };
-  const source: AnalysisReportSource = {
-    type: "session",
-    id: report.sessionId,
-    label: "Current conversation",
-  };
-  const hasBioContent = sessionHasBioAnalysisContent(input.context);
-  if (!hasBioContent) {
-    return hasReportSectionContent(report.sections)
-      ? { ...report, markdown: renderReportMarkdown(report.title, report.sections) }
-      : {
-          ...report,
-          sections: SECTION_DEFS.map((section) => makeEmptySection(section.id, section.title)),
-          sources: [],
-          changes: [],
-          markdown: "",
-        };
-  }
-
-  const objective = firstAnalysisUserText(input.context) || firstUserText(input.context);
-  const files = extractOutputFiles(input.context);
-  const signals = collectSessionSignals(input.context);
-  const topic = input.topic ?? (objective ? cleanText(objective).slice(0, 80) : "");
-  const figuresMarkdown = representativeFigures(files);
-  const resultsMarkdown = combineMarkdown([
-    signals.results.length > 0 ? bullets(signals.results) : "",
-    figuresMarkdown,
-  ]);
-
-  if (input.topic) {
-    let nextReport: AnalysisReport = report;
-    const addTopicUpdate = (section: string, markdown: string, sources: AnalysisReportSource[] = []) => {
-      const cleaned = markdown.trim();
-      if (!cleaned) return;
-      nextReport = applyReportUpdate(nextReport, {
-        topic,
-        section,
-        action: "append",
-        status: "draft",
-        markdown: cleaned,
-        sources,
-        note: `Added current-topic summary for ${topic}.`,
-      }, `${report.sessionId}:${topic}:${section}:${stableHash(cleaned)}`);
-    };
-
-    addTopicUpdate("objective", objective ? `- ${objective}` : "", objective ? [source] : []);
-    addTopicUpdate("input_data", files.length > 0
-      ? [
-          "Detected data or result paths mentioned in this topic:",
-          "",
-          outputTable(files.slice(0, 12)),
-        ].join("\n")
-      : "", files.length > 0 ? [source] : []);
-    addTopicUpdate("methods", signals.methods.length > 0 ? bullets(signals.methods) : "", signals.methods.length > 0 ? [source] : []);
-    addTopicUpdate("quality_control", signals.qc.length > 0 ? bullets(signals.qc) : "", signals.qc.length > 0 ? [source] : []);
-    addTopicUpdate("results", resultsMarkdown, resultsMarkdown ? [source] : []);
-    addTopicUpdate("interpretation", signals.interpretation.length > 0 ? bullets(signals.interpretation) : "", signals.interpretation.length > 0 ? [source] : []);
-    addTopicUpdate("outputs", files.length > 0 ? outputTable(files) : "", files.length > 0 ? [source] : []);
-    addTopicUpdate("reproducibility", signals.reproducibility.length > 0 ? bullets(signals.reproducibility) : "", signals.reproducibility.length > 0 ? [source] : []);
-    return nextReport;
-  }
-
-  updateSection(
-    report,
-    "objective",
-    objective ? withTopicPrefix(`- ${objective}`, topic) : "",
-    objective ? "draft" : "draft",
-    objective ? [source] : []
-  );
-  updateSection(
-    report,
-    "input_data",
-    files.length > 0
-      ? withTopicPrefix([
-          "Detected data or result paths mentioned in this session:",
-          "",
-          outputTable(files.slice(0, 12)),
-        ].join("\n"), topic)
-      : "",
-    files.length > 0 ? "draft" : "draft",
-    files.length > 0 ? [source] : []
-  );
-  updateSection(report, "methods", signals.methods.length > 0 ? withTopicPrefix(bullets(signals.methods), topic) : "", signals.methods.length > 0 ? "draft" : "draft", signals.methods.length > 0 ? [source] : []);
-  updateSection(report, "quality_control", signals.qc.length > 0 ? withTopicPrefix(bullets(signals.qc), topic) : "", signals.qc.length > 0 ? "draft" : "draft", signals.qc.length > 0 ? [source] : []);
-  updateSection(report, "results", resultsMarkdown ? withTopicPrefix(resultsMarkdown, topic) : "", resultsMarkdown ? "draft" : "draft", resultsMarkdown ? [source] : []);
-  updateSection(report, "interpretation", signals.interpretation.length > 0 ? withTopicPrefix(bullets(signals.interpretation), topic) : "", signals.interpretation.length > 0 ? "draft" : "draft", signals.interpretation.length > 0 ? [source] : []);
-  updateSection(report, "outputs", files.length > 0 ? withTopicPrefix(outputTable(files), topic) : "", files.length > 0 ? "draft" : "draft", files.length > 0 ? [source] : []);
-  updateSection(report, "reproducibility", signals.reproducibility.length > 0 ? withTopicPrefix(bullets(signals.reproducibility), topic) : "", signals.reproducibility.length > 0 ? "draft" : "draft", signals.reproducibility.length > 0 ? [source] : []);
-
-  if (hasReportSectionContent(report.sections)) {
-    report.sources = [source];
-    report.changes = [
-      {
-        id: `change-${Date.now()}`,
-        timestamp: nowIso(),
-        title: "Generated from conversation",
-        detail: "Refreshed the analysis report from the current session, keeping only analysis objectives, methods, results, interpretations, outputs, and reproducibility notes.",
-      },
-      ...report.changes,
-    ].slice(0, 50);
-  }
-  return report;
-}
-
-export function renderReportMarkdown(title: string, sections: AnalysisReportSection[]): string {
-  const contentSections = sections.filter((section) => normalizeEmptyMarkdown(section.markdown).length > 0);
-  if (contentSections.length === 0) return "";
-
-  const body = contentSections.map((section) => {
-    const status = section.status === "verified"
-      ? "verified"
-      : section.status === "outdated"
-      ? "outdated"
-      : section.status === "needs_review"
-      ? "needs review"
-      : "draft";
-    const content = normalizeEmptyMarkdown(section.markdown);
-    return `## ${section.title}\n\n_Status: ${status}_\n\n${content}`;
-  });
-  return [`# ${title || "Analysis Report"}`, ...body].join("\n\n");
-}

package/lib/report-update-parser.ts

@@ -1,66 +0,0 @@
-import type { AnalysisReportUpdate } from "@/lib/report-store";
-
-export interface ParsedReportUpdate {
-  update: AnalysisReportUpdate;
-  raw: string;
-}
-
-const REPORT_FENCE_RE = /```(?:analysis-report-update|report-update)\s*\n([\s\S]*?)```/gi;
-
-function isRecord(value: unknown): value is Record<string, unknown> {
-  return typeof value === "object" && value !== null && !Array.isArray(value);
-}
-
-function normalizeStatus(value: unknown): AnalysisReportUpdate["status"] | undefined {
-  if (value === "draft" || value === "verified" || value === "outdated" || value === "needs_review") return value;
-  if (value === "needs review") return "needs_review";
-  return undefined;
-}
-
-function normalizeAction(value: unknown): AnalysisReportUpdate["action"] | undefined {
-  return value === "replace" ? "replace" : value === "append" ? "append" : undefined;
-}
-
-function parseUpdate(rawJson: string): AnalysisReportUpdate | null {
-  try {
-    const parsed = JSON.parse(rawJson) as unknown;
-    if (!isRecord(parsed)) return null;
-    return {
-      topic: typeof parsed.topic === "string" ? parsed.topic : undefined,
-      section: typeof parsed.section === "string" ? parsed.section : undefined,
-      action: normalizeAction(parsed.action),
-      status: normalizeStatus(parsed.status),
-      markdown: typeof parsed.markdown === "string" ? parsed.markdown : undefined,
-      sources: Array.isArray(parsed.sources) ? parsed.sources as AnalysisReportUpdate["sources"] : undefined,
-      invalidates: Array.isArray(parsed.invalidates)
-        ? parsed.invalidates.filter((item): item is string => typeof item === "string")
-        : undefined,
-      note: typeof parsed.note === "string" ? parsed.note : undefined,
-    };
-  } catch {
-    return null;
-  }
-}
-
-export function parseReportUpdates(content: string): ParsedReportUpdate[] {
-  const updates: ParsedReportUpdate[] = [];
-  for (const match of content.matchAll(REPORT_FENCE_RE)) {
-    const raw = match[0];
-    const body = match[1]?.trim() ?? "";
-    const update = parseUpdate(body);
-    if (update) updates.push({ update, raw });
-  }
-  return updates;
-}
-
-export function stripReportUpdateFences(content: string): string {
-  return content
-    .replace(REPORT_FENCE_RE, "")
-    .replace(/\n{3,}/g, "\n\n")
-    .trim();
-}
-
-export function hasReportUpdateFence(content: string): boolean {
-  REPORT_FENCE_RE.lastIndex = 0;
-  return REPORT_FENCE_RE.test(content);
-}