v0.7: \u4fee\u590d PDF \u5f15\u6587\u7f16\u53f7\u4e0d\u5bf9\u5e94 + \u5c01\u9762\u91cd\u590d

\u4e24\u4e2a P0 bug \u4fee\u590d\uff1a

1. \u5f15\u6587\u7f16\u53f7\u5931\u914d
   \u5148\u524d\u7b56\u7565\uff1a\u53c2\u8003\u6587\u732e\u533a\u6309\u6b63\u6587\u51fa\u73b0\u987a\u5e8f\u91cd\u7f16\u53f7\u4e3a [1]/[2]/...\uff0c\u5bfc\u81f4\u6b63\u6587\u4e2d\u4e0a\u6807\u7684 [src_E43]
   \u4e0e\u53c2\u8003\u6587\u732e\u533a\u7684 [27] \u5b8c\u5168\u5bf9\u4e0d\u4e0a\u3002
   \u65b0\u7b56\u7565\uff1a\u53c2\u8003\u6587\u732e\u6761\u76ee\u76f4\u63a5\u7528\u539f\u59cb src_id \u4f5c\u7f16\u53f7\uff08\u5982 [src_E43] ...\uff09\uff0c
   \u6309\u5b57\u6bcd\u6570\u5b57\u6392\u5e8f\u5206\u7ec4\u5c55\u793a\u3002\u6b63\u6587\u548c\u53c2\u8003\u6587\u732e\u540c key\uff0c\u4e00\u773c\u5bf9\u5e94\u3002
   \u540c\u65f6\u628a\u7f3a\u5931\u7684 src_id\uff08sources.jsonl \u91cc\u6ca1\u7684\uff09\u5355\u72ec\u5217\u5728\u300c\u672a\u627e\u5230\u6765\u6e90\u300d
   \u7ae0\u8282\uff0c\u6a59\u8272\u8b66\u793a\uff0c\u8868\u660e\u662f\u539f\u59cb\u62a5\u544a\u7684\u8d28\u91cf\u95ee\u9898\u3001\u800c\u975e\u6e32\u67d3\u95ee\u9898\u3002
   \u9876\u90e8\u65b0\u589e\u300c\u5f15\u6587\u5065\u5eb7\u72b6\u6001\u300d\u5c0f\u7ed3\uff08\u6b63\u6587\u5f15\u7528X\u3001\u6536\u5f55Y\u3001\u7f3a\u5931Z\uff09\u3002

2. \u5c01\u9762\u91cd\u590d\uff08\u622a\u56fe\uff1a\u526f\u6807\u9898 + Confidentiality/Date/Version \u4ecd\u5728\u6b63\u6587\u9996\u9875\uff09
   \u539f\u56e0\uff1a\u539f\u8df3\u8fc7\u903b\u8f91\u662f\u201c\u8df3\u9996\u4e2a H1 \u2192 \u8df3\u5339\u914d is_cover_frontmatter \u7684 p\u201d\u3002
   \u526f\u6807\u9898\u662f\u52a0\u7c97\u6bb5\uff08**...**\uff09\uff0c\u4e0d\u542b "Confidentiality/Date" \u7b49\u5173\u952e\u8bcd\uff0c
   \u5339\u914d\u4e0d\u4e0a\u5c31\u89e6\u53d1\u300c\u5c01\u9762\u7ed3\u675f\u300d\u903b\u8f91\uff0c\u540e\u7eed\u5143\u4fe1\u606f\u6bb5\u4e5f\u6240\u4ee5\u5c31\u6f0f\u5305\u4e86\u3002
   \u65b0\u7b56\u7565\uff1a\u7b80\u5316\u4e3a\u300c\u6253\u8868\u4ece\u7b2c\u4e00\u4e2a H2/H3 \u5f00\u59cb\u8fed\u4ee3\u300d\uff0c\u524d\u9762\u7684 block \u5168\u90e8\u4e22\u6389\u3002
   \u7406\u7531\uff1a\u5c01\u9762\u5df2\u7531 build_cover \u4ece manifest \u72ec\u7acb\u751f\u6210\uff0c\u6b63\u6587\u5f00\u5934\u5728\u7b2c\u4e00\u4e2a H2
   \uff08\u201c## \u514d\u8d23\u58f0\u660e\u201d\uff09\u524d\u7684\u4efb\u4f55\u5185\u5bb9\u90fd\u662f\u5197\u4f59\u7684\u5c01\u9762\u5143\u4fe1\u606f\u3002

\u9a8c\u8bc1\uff1a\u91cd\u8dd1 PDF\uff0c\u7528 pypdf \u63d0\u53d6\u7b2c 1-2 \u9875\u548c\u53c2\u8003\u6587\u732e\u9875\u786e\u8ba4\u4e24\u4e2a bug \u90fd\u5df2\u6d88\u5931\u3002

\u9879\u76ee\u65b0\u589e pypdf \u4f9d\u8d56\uff08\u5de5\u5177\u7c7b\uff0c\u9a8c\u8bc1 PDF \u6587\u672c\u5185\u5bb9\u7528\uff09\u3002

Co-authored-by: User <human>

.opencode/templates/report-template.py

@@ -812,6 +812,19 @@ def format_gb7714(rec: dict) -> str:
     return body
 
 
+def _sort_src_id(sid: str) -> tuple:
+    """为 src_id 生成排序键：按字母段分组（A/B/C/E/...），组内按数字升序。"""
+    m = re.match(r"src_([A-Za-z]+)?(\d+)?([A-Za-z0-9_\-]*)", sid)
+    if not m:
+        return ("~", 0, sid)
+    alpha, num, rest = m.group(1) or "", m.group(2) or "0", m.group(3) or ""
+    try:
+        num_int = int(num)
+    except ValueError:
+        num_int = 0
+    return (alpha, num_int, rest)
+
+
 def build_references(
     blocks: List[Block],
     sources_path: Optional[Path],
@@ -819,7 +832,12 @@ def build_references(
 ) -> List:
     """生成参考文献段落。
 
-    引用顺序：按正文首次出现的先后排列（GB/T 7714 顺序编码制）。
+    v0.7 改变：**不再按出现顺序重编号**（之前会导致正文中 `[src_E43]` 和参考文献
+    区的 `[27]` 对不上）。改为：
+    - 参考文献条目直接用原始 `src_id` 作为编号（如 `[src_E43] Alnylam..., 2025.`）
+    - 按 src_id 字母数字排序分组
+    - 缺失的 src_id 单独一段列出，明显标注供人工核查
+    - 顶部给一条"引文健康状态"小结
     """
     story: list = []
     story.append(Paragraph("参考文献", styles["h1"]))
@@ -835,31 +853,67 @@ def build_references(
         ))
         return story
 
-    if not sources:
+    cited_set = set(cited_ids)
-        # 至少列出所有被引用的 ID，供人工回填
+    matched = [sid for sid in cited_ids if sid in sources]
+    missing = [sid for sid in cited_ids if sid not in sources]
+    # sources.jsonl 里有但正文没引用的——列为"备选"不展示，只统计
+    unused = [sid for sid in sources if sid not in cited_set]
+
+    # 头部健康状态
+    health = (
+        f"正文引用 <b>{len(cited_set)}</b> 条独立标识符；"
+        f"sources.jsonl 收录 <b>{len(sources)}</b> 条，"
+        f"<b>{len(matched)}</b> 条可对应，"
+        f"<b>{len(missing)}</b> 条在 sources.jsonl 中未找到。"
+    )
+    if unused:
+        health += f" 另有 {len(unused)} 条收录来源未在正文中引用，已省略展示。"
+    story.append(Paragraph(
+        f"<font color='#6b7280' size=8>引文健康状态：{health}</font>",
+        styles["caption"],
+    ))
+    story.append(Spacer(1, 0.3 * cm))
+
+    # 主列表：按 src_id 字母数字排序
+    if matched:
         story.append(Paragraph(
-            f"（未找到 sources.jsonl 或其内容为空。以下为正文出现的 {len(cited_ids)} 个引用标识符）",
+            "<b>收录来源</b>",
+            styles["h3"],
+        ))
+        for sid in sorted(matched, key=_sort_src_id):
+            rec = sources[sid]
+            text = format_gb7714(rec)
+            # 编号就是原始 sid，便于和正文中的 [src_E43] 上标对应
+            entry = f"<b>[{sid}]</b>  {text}"
+            story.append(Paragraph(entry, styles["footnote"]))
+
+    # 缺失列表：明显标注
+    if missing:
+        story.append(Spacer(1, 0.4 * cm))
+        story.append(Paragraph(
+            f"<b>未找到来源（{len(missing)} 条）</b>",
+            styles["h3"],
+        ))
+        story.append(Paragraph(
+            "<font color='#b45309' size=8>"
+            "以下标识符在正文中出现但未在 <code>sources.jsonl</code> 中找到对应记录。"
+            "可能是编写阶段的占位符未回填，或原始研究员引用不规范，请核查后补充。"
+            "</font>",
             styles["caption"],
         ))
-        for i, sid in enumerate(cited_ids, 1):
+        # 按字母数字排序分组展示，一行三个，节省篇幅
-            story.append(Paragraph(f"[{i}] {sid}", styles["footnote"]))
+        sorted_missing = sorted(missing, key=_sort_src_id)
-        return story
+        # 每 4 个一行
-
+        row_size = 4
-    missing: list[str] = []
+        for k in range(0, len(sorted_missing), row_size):
-    for i, sid in enumerate(cited_ids, 1):
+            chunk = sorted_missing[k : k + row_size]
-        rec = sources.get(sid)
+            row_text = "　　".join(f"[{sid}]" for sid in chunk)
-        if not rec:
-            missing.append(sid)
             story.append(Paragraph(
-                f"[{i}] {sid}（来源记录缺失，请核查 sources.jsonl）",
+                f"<font color='#b45309'>{row_text}</font>",
                 styles["footnote"],
             ))
-            continue
-        text = format_gb7714(rec)
-        # 前面加序号，后面追加 [sid] 便于正文回溯
-        entry = f"[{i}] {text}  <font color='#6b7280' size=7>【{sid}】</font>"
-        story.append(Paragraph(entry, styles["footnote"]))
 
+    # 打印到 stderr
     if missing:
         print(
             f"WARNING: {len(missing)} cited src_ids not found in sources.jsonl: "
@@ -955,52 +1009,24 @@ def build_body(
     - H1 triggers PageBreak；H2/H3 keepWithNext；表格 splitByRow
     """
     story: list = []
-    first_h1_seen = False           # 是否已跳过正文首个 H1
-    skipping_cover_meta = False     # 是否在吞掉封面元信息段
-
-    # Summary 样式
     in_summary = False
 
-    # 准备跳过标志：标题级别下一个 "目录""参考文献" 见到时替换掉它（包含其下紧跟的占位段）
+    # 第一步：跳过"封面块"——从正文开头一直跳到第一个 H2/H3 前。
-    # 采用简单索引遍历以便向前看。
+    # 封面块 = 首个 H1（主标题） + 副标题（加粗 p） + 元信息段（Confidentiality/Date/Version） + 分隔线（hr）。
-    i = 0
+    # 这些已由 build_cover 从 manifest 独立生成，正文里再出现就是重复。
+    # 规则简单可靠：跳过所有 block 直到遇到第一个 H2/H3（如 "## 免责声明"）。
     n = len(blocks)
+    first_section_idx = n
+    for k, b in enumerate(blocks):
+        if b.kind in ("h2", "h3"):
+            first_section_idx = k
+            break
+    i = first_section_idx  # 从第一个 section 开始处理
+
     while i < n:
         block = blocks[i]
 
-        # --- 跳过正文首个 H1（封面标题）+ 紧跟的元信息/hr ---
+        # --- H1 处理（非首个；本循环内 first_section_idx 之后的 H1 都是真正的章节 H1）---
-        if not first_h1_seen and block.kind == "h1":
-            first_h1_seen = True
-            skipping_cover_meta = True
-            i += 1
-            continue
-        if skipping_cover_meta:
-            # 吞掉 p（元信息）、hr、quote（副标题可能被当成加粗段）
-            # 遇到 h1/h2/h3 就停止吞
-            if block.kind in ("h1", "h2", "h3"):
-                skipping_cover_meta = False
-                # 不 continue，让当前 block 正常处理
-            elif block.kind == "p" and is_cover_frontmatter(block.content):
-                i += 1
-                continue
-            elif block.kind in ("hr", "quote", "p", "bullet"):
-                # 第一个 hr 标记封面结束
-                if block.kind == "hr":
-                    skipping_cover_meta = False
-                    i += 1
-                    continue
-                # 普通段落：如果不是封面元信息，就认为封面已结束
-                if block.kind == "p":
-                    skipping_cover_meta = False
-                    # fall through to normal handling
-                else:
-                    i += 1
-                    continue
-            else:
-                i += 1
-                continue
-
-        # --- H1 处理（非首个）---
         if block.kind == "h1":
             story.append(PageBreak())
             content = block.content

pyproject.toml

@@ -19,6 +19,7 @@ dependencies = [
     "python-dateutil>=2.9.0",
     "PyYAML>=6.0.1",
     "rich>=13.7.0",
+    "pypdf>=6.10.2",
 ]
 
 [project.optional-dependencies]

uv.lock

@@ -374,6 +374,7 @@ dependencies = [
     { name = "pandas", version = "2.3.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
     { name = "pandas", version = "3.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
     { name = "pillow" },
+    { name = "pypdf" },
     { name = "python-dateutil" },
     { name = "pyyaml" },
     { name = "reportlab" },
@@ -397,6 +398,7 @@ requires-dist = [
     { name = "numpy", specifier = ">=1.26.0" },
     { name = "pandas", specifier = ">=2.1.0" },
     { name = "pillow", specifier = ">=10.0.0" },
+    { name = "pypdf", specifier = ">=6.10.2" },
     { name = "pytest", marker = "extra == 'dev'", specifier = ">=7.4.0" },
     { name = "python-dateutil", specifier = ">=2.9.0" },
     { name = "pyyaml", specifier = ">=6.0.1" },
@@ -1292,6 +1294,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/10/bd/c038d7cc38edc1aa5bf91ab8068b63d4308c66c4c8bb3cbba7dfbc049f9c/pyparsing-3.3.2-py3-none-any.whl", hash = "sha256:850ba148bd908d7e2411587e247a1e4f0327839c40e2e5e6d05a007ecc69911d", size = 122781, upload-time = "2026-01-21T03:57:55.912Z" },
 ]
 
+[[package]]
+name = "pypdf"
+version = "6.10.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "typing-extensions", marker = "python_full_version < '3.11'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/7b/3f/9f2167401c2e94833ca3b69535bad89e533b5de75fefe4197a2c224baec2/pypdf-6.10.2.tar.gz", hash = "sha256:7d09ce108eff6bf67465d461b6ef352dcb8d84f7a91befc02f904455c6eea11d", size = 5315679, upload-time = "2026-04-15T16:37:36.978Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/0c/d6/1d5c60cc17bbdf37c1552d9c03862fc6d32c5836732a0415b2d637edc2d0/pypdf-6.10.2-py3-none-any.whl", hash = "sha256:aa53be9826655b51c96741e5d7983ca224d898ac0a77896e64636810517624aa", size = 336308, upload-time = "2026-04-15T16:37:34.851Z" },
+]
+
 [[package]]
 name = "pytest"
 version = "9.0.3"