cfc/cfc-langgraph/app/parsers/pdf_parser.py

"""
菌群报告 PDF 解析器
从 extract_full_report_v5.py 提取核心逻辑，封装为可调用函数
"""
import os
import re
from PyPDF2 import PdfReader

# === 常量 ===
# Kangxi 部首 → CJK 统一汉字（与 extract_full_report_v5.py 完全一致）
RADICAL_MAP = {
    '\u2f18': '卜', '\u2f1f': '土', '\u2f24': '大', '\u2f26': '子',
    '\u2f29': '小', '\u2f2d': '山', '\u2f32': '干', '\u2f3c': '心',
    '\u2f42': '文', '\u2f46': '无', '\u2f4a': '木', '\u2f50': '比',
    '\u2f54': '水', '\u2f55': '火', '\u2f5c': '牛', '\u2f5f': '玉',
    '\u2f60': '瓜', '\u2f62': '甘', '\u2f63': '生', '\u2f64': '用',
    '\u2f69': '白', '\u2f6a': '皮', '\u2f6c': '目', '\u2f6f': '石',
    '\u2f75': '竹', '\u2f76': '米', '\u2f7a': '羊', '\u2f7b': '羽',
    '\u2f7c': '老', '\u2f7f': '耳', '\u2f81': '肉', '\u2f90': '衣',
    '\u2f95': '谷', '\u2f96': '豆', '\u2f9d': '身', '\u2fa6': '金',
    '\u2faf': '面', '\u2fb2': '韭', '\u2fb9': '香', '\u2fca': '黑',
    '\u2ec9': '贝', '\u2edd': '食', '\u2ee2': '马', '\u2ee5': '鱼',
    '\u2ee8': '麦', '\u2ee9': '黄', '\u2ef0': '龙',
    # 氏 radical U+2F52 → U+6C0F
    '\u2f52': '氏',
}

KNOWN_MACRO = ['碳水化合物', '蛋白质', '脂肪', '纤维素', '乳制品']
KNOWN_AMINO = ['苏氨酸', '异亮氨酸', '亮氨酸', '赖氨酸', '蛋氨酸', '胱氨酸',
    '苯丙氨酸', '酪氨酸', '缬氨酸', '组氨酸', '丙氨酸', '丝氨酸', '甘氨酸',
    '脯氨酸', '谷氨酸', '天门冬氨酸', '天冬氨酸', '天冬酰胺', '谷氨酰胺',
    '精氨酸', '色氨酸']
KNOWN_VITAMINS = ['维生素A', '维生素B1', '维生素B2', '维生素B5', '维生素B6',
    '叶酸', '维生素B12', '维生素C', '维生素D', '维生素K2', '维生素E']
KNOWN_TRACE = ['铁', '锌']
KNOWN_DISEASE_RISKS = ['炎症性肠炎', '肠易激综合征', '感染性腹泻', '自闭症',
    '抑郁症', '甲状腺疾病', '肺部感染或疾病', '自体免疫病', '结直肠癌',
    '肥胖', '便秘', '过敏', '失眠', '肝病', '肾病', '胃病', '胆病',
    '心脑血管疾病', 'II型糖尿病']
KNOWN_BARRIER = ['肠道炎症水平', '肠道产气', '肠道屏障', '脂多糖LPS',
    '次级胆汁酸', '对甲酚（p-Cresol）', '吲哚', '苯酚', '腐胺', '硫化氢', '尸胺']
KNOWN_SCFA = ['丁酸盐（Butyrate）', '丙酸盐（Propionate）', '乙酸盐（Acetate）', '异戊酸盐（Isovaleric）']
KNOWN_NEURO = ['血清素（5-HT）', 'γ-氨基丁酸（GABA）', '谷氨酸（Glutamate）',
    '色氨酸（Tryptophan）', 'DOPAC', '多巴胺', '组胺（Histamine）', '一氧化氮',
    '喹啉（Quinolinic）', '维生素K2', '肌醇（Inositol）', '肾上腺素',
    '去甲肾上腺素', '乙酰胆碱', '皮质醇']
KNOWN_ANTIBIOTICS = ['β-内酰胺酶类', '氨基糖苷类', '大环内酯类', '呋喃类',
    '喹诺酮类', '磺胺类', '甲氧苄啶类', '氯霉素类', '四环素类']
KNOWN_PATHOGENS = ['幽门螺杆菌', '艰难梭菌', '沙门氏菌', '志贺氏菌', '弯曲杆菌']

# === 菌群表标题（完整版 extract_full_report_v5.py 移植） ===
BACTERIA_TABLE_TITLES = [
    '核心菌属构成表', '益生菌', '有害菌属构成表',
    '其它重要菌属构成表', '病原菌属构成表',
]
PHYLUM_TABLE_TITLES = ['菌门构成表', '菌群门水平构成表', '门水平菌群构成']
CLASS_TABLE_TITLES = ['菌纲构成表', '菌群纲水平构成表', '纲水平菌群构成']
ORDER_TABLE_TITLES = ['菌目构成表', '菌群目水平构成表', '目水平菌群构成']
FAMILY_TABLE_TITLES = ['菌科构成表', '菌群科水平构成表', '科水平菌群构成']
GENUS_TABLE_TITLES = ['菌属构成表', '菌群属水平构成表', '属水平菌群构成']
SPECIES_TABLE_TITLES = ['菌种构成表', '菌群种水平构成表', '种水平菌群构成']
DISEASE_BACTERIA_TITLES = [
    '肥胖相关菌', '便秘相关菌', '抑郁相关菌', '过敏相关菌',
    '腹胀相关菌', '失眠相关菌', '肠道健康相关菌',
    '多动症相关菌', '自闭症相关菌',
]

# === 食物推荐表（完整版 extract_full_report_v5.py 移植） ===
COLUMNS_FOOD = ['名称', '分类', '推荐指数', '能量KJ', '蛋白g', '脂肪g',
    '碳水化合物g', '淀粉g', '总膳食纤维g', '胆固醇mg']
KNOWN_CATS = ['主食', '乳制品', '干果', '坚果', '快餐', '水产品',
    '水果', '汤', '肉类', '蔬菜', '豆类及豆制品', '蛋类', '饮料']
FOOD_SKIP_TEXTS = [
    '根据您的肠道菌群', '分值从-100', '食物推荐考虑', '食物推荐是综合',
    '需要注意的是', '本饮食推荐', '该饮食推荐根据', '后续表格中的营养',
    '16S 高通量测序', '基于机器学习和', '肠道菌群健康检测报告说明',
    '检测方法及局限性', '数据分析及模型', '结果解读及使用',
    '影响因素说明', '建议将检测结果', '营养建议说明',
    '重要提示', '推荐食物清单', '实际食用时需结合', '如有特殊疾病',
    '免责声明', '本检测报告仅供', '以上模型预测', '正常范围的定义',
    '募极生物',
]


def norm(s):
    return ''.join(RADICAL_MAP.get(c, c) for c in s)


def detect_format(lines):
    """检测 triplet / inline 格式"""
    text = '\n'.join(lines)
    has_triplet = '指标范围' in text and '疾病风险评估' in text
    for line in lines:
        if len(line) > 15 and re.search(r'[\u4e00-\u9fff]+[\d.]+[\u4e00-\u9fff/]+', line):
            for known in KNOWN_DISEASE_RISKS:
                if known in line:
                    return 'inline'
    return 'triplet' if has_triplet else 'inline'


def extract_text(file_path):
    """读取 PDF 并提取文本"""
    reader = PdfReader(file_path)
    lines = []
    for page in reader.pages:
        text = norm(page.extract_text() or '')
        for line in text.split('\n'):
            ls = line.strip()
            if ls:
                lines.append(ls)
    return lines


def parse_overview(lines):
    """提取报告概述"""
    text = '\n'.join(lines)
    r = {}
    m = re.search(r'编号[：:\s]*(\d+)', text)
    if m: r['report_number'] = m.group(1)
    m = re.search(r'姓名[：:\s]*([\u4e00-\u9fff]{2,10})', text)
    if m: r['person_name'] = re.sub(r'(编号|年龄|性别|备注|肠道).*', '', m.group(1))[:4]
    m = re.search(r'年龄[：:\s]*(\d+)', text)
    if m: r['age'] = int(m.group(1))
    m = re.search(r'性别[：:\s]*([\u4e00-\u9fff])', text)
    if m: r['gender'] = 'male' if m.group(1) == '男' else 'female'
    for kw in ['健康总分', '菌群健康', '慢病控制', '营养均衡', '肠道菌群平衡',
               '菌群多样性', '有益菌', '有害菌', '核心菌属']:
        m = re.search(rf'{kw}\s*(\d+)', text)
        if m: r[kw] = int(m.group(1))
    m = re.search(r'肠道预测年龄[：:\s]*([\d.]+)', text)
    if m: r['gut_age'] = m.group(1)
    m = re.search(r'肠型[：:\s]*(\S+)', text)
    if m: r['gut_type'] = m.group(1)
    return r


def parse_triplet_until(lines, stop_markers):
    """三元组解析：3行一组 名称/数值/状态"""
    results = []
    i = 0
    while i < len(lines):
        if any(lines[i] == sm or lines[i].startswith(sm) for sm in stop_markers):
            break
        if lines[i] in ('指标范围', '名称', '丰度', '评估'):
            i += 1
            continue
        name = lines[i]
        if i + 2 >= len(lines): break
        val = lines[i + 1]
        status = lines[i + 2]
        if re.match(r'^-?\d+\.?\d*$', val):
            results.append({'name': name, 'value': val, 'status': status})
            i += 3
        else:
            i += 1
    return results


def parse_report_pdf(file_path: str) -> dict:
    """主函数：解析 PDF 返回结构化数据"""
    lines = extract_text(file_path)
    full_text = '\n'.join(lines)

    # 指纹检测：北京菌群报告
    if detect_beijing_format(full_text):
        return _parse_beijing_report(file_path)

    fmt = detect_format(lines)
    result = {'format': fmt, 'overview': parse_overview(lines)}

    # 疾病风险评估
    for i, line in enumerate(lines):
        if '疾病风险评估' in line and '注' not in line:
            risks = parse_triplet_until(lines[i+1:],
                ['主要营养评估', '氨基酸评估', '维生素评估', '微量元素评估', '抗生素风险评估'])
            result['disease_risks'] = [r for r in risks if '注' not in r['name']]
            break

    # 主要营养评估
    for i, line in enumerate(lines):
        if '主要营养评估' in line:
            nutrients = parse_triplet_until(lines[i+1:], ['氨基酸评估'])
            result['nutrition'] = nutrients[:5]
            break

    # 氨基酸评估
    for i, line in enumerate(lines):
        if '氨基酸评估' in line:
            aminos = parse_triplet_until(lines[i+1:], ['维生素评估', '微量元素评估'])
            result['amino_acids'] = aminos
            break

    # 维生素评估
    for i, line in enumerate(lines):
        if '维生素评估' in line:
            vits = parse_triplet_until(lines[i+1:], ['微量元素评估', '抗生素风险评估'])
            result['vitamins'] = [r for r in vits if '维生素' in r['name']]
            result['trace_elements'] = [r for r in vits if '维生素' not in r['name']]
            break

    # 菌群检出详细列表（核心/益生菌/有害菌/病原菌 + 门纲目科属种）
    bacteria_tables = _extract_bacteria_tables(file_path)
    result['菌群检出详细列表'] = bacteria_tables

    # 个体化食物推荐表（保留原始键名与结构）
    food_rows, food_fmt = _extract_food_rows(file_path)
    result['个体化食物推荐表'] = {
        '格式': food_fmt,
        '条目数': len(food_rows),
        '数据': food_rows
    }

    # 统一结构：北京报告特有字段（标准报告为空）
    result['肠道微生物健康指数'] = {}
    result['菌群多样性'] = {}
    result['肠道黏膜屏障'] = {}
    result['菌群表型评估'] = {}
    result['短链脂肪酸合成能力'] = {}
    result['肠道菌群精准分布'] = []
    result['营养物质及营养素代谢评估'] = {}
    result['抗生素风险评估'] = {}
    result['毒性物质清除能力评估'] = {}
    result['趣味肠菌评估'] = {}
    result['胃肠道感染病原体'] = []
    result['健康整体评估'] = {}
    result['肠道菌群主要检测结果'] = {}

    return result


def parse_report_pdf_with_fallback(file_path: str) -> dict:
    """算法解析 + 简单校验，返回结构化数据"""
    result = parse_report_pdf(file_path)
    # 简单校验：如果关键字段缺失，标记为解析不完整
    if not result.get('overview', {}).get('overallScore') and \
       not result.get('overview', {}).get('健康总分'):
        result['_parse_incomplete'] = True
    return result


def _parse_bacteria_table(reader, pages_text, full_text, title, fmt, skip_header=False):
    """从PDF中解析一个菌群表格（移植自 extract_full_report_v5.py）"""
    results = []
    sidx = full_text.find(title)
    if sidx == -1:
        return results

    # 病原菌检出表特殊处理：找"仅列出检出的病原菌"（跳过前面的说明文字中的"病原菌"）
    if title == '病原菌':
        better_sidx = full_text.find('仅列出检出的病原菌')
        if better_sidx != -1:
            sidx = better_sidx

    # 找表格结束位置（下一个标题或页尾）
    end_pos = len(full_text)
    for t in (BACTERIA_TABLE_TITLES + PHYLUM_TABLE_TITLES + CLASS_TABLE_TITLES
              + ORDER_TABLE_TITLES + FAMILY_TABLE_TITLES + GENUS_TABLE_TITLES
              + SPECIES_TABLE_TITLES + DISEASE_BACTERIA_TITLES
              + ['指标范围', '个体化食物推荐表', '报告总结', '健康总分']):
        if t == title:
            continue
        ei = full_text.find(t, sidx + len(title))
        if ei != -1 and ei < end_pos:
            end_pos = ei

    region = full_text[sidx:end_pos]

    # 检测区域实际格式：如果换行数很少(<3)则是inline格式，即使全局fmt=triplet
    lines_from_region = [l.strip() for l in region.split('\n') if l.strip()]
    actual_fmt = fmt
    if fmt == 'triplet' and len(lines_from_region) <= 5:
        actual_fmt = 'inline'

    if actual_fmt == 'triplet':
        # 三元组格式：每个字段单独一行
        lines = [l.strip() for l in region.split('\n') if l.strip()]
        start = 0
        for i, line in enumerate(lines):
            if line == '名称':
                start = i + 1
                break
            if line.startswith('名称'):
                if skip_header:
                    start = i + 1
                break

        i = start
        while i < len(lines):
            name = lines[i]
            if not name or len(name) <= 1 or name in ['说明', '检测结果', '结果解释', '建议']:
                i += 1
                continue
            if name.startswith('说明：') or name.startswith('改善方式'):
                i += 1
                continue
            if len(name) > 80:
                i += 1
                continue

            # 找丰度%
            if i + 1 < len(lines) and re.match(r'^[\d]+\.?[\d]*%?$|^ND$', lines[i + 1]):
                pct = lines[i + 1]
                normal_range = ''
                pop_level = ''
                detection_rate = ''
                desc = ''
                j = i + 2
                # 正常范围 (允许小数，如 0.06-6.96, 0.03-3.07)
                if j < len(lines) and re.match(r'^[\d]+\.?[\d]*-[\d]+\.?[\d]*$', lines[j]):
                    normal_range = lines[j]
                    j += 1
                # 人群水平% (允许小数，如 15.66%)
                if j < len(lines) and re.match(r'^\d+\.?\d*%$', lines[j]):
                    pop_level = lines[j]
                    j += 1
                # 检出率%
                if j < len(lines) and re.match(r'^\d+\.?\d*%$', lines[j]):
                    detection_rate = lines[j]
                    j += 1
                # 说明
                if j < len(lines) and lines[j].startswith('说明'):
                    desc = lines[j]
                    j += 1
                # 改善方式
                if j < len(lines) and lines[j].startswith('改善方式'):
                    if desc:
                        desc += ' | ' + lines[j]
                    else:
                        desc = lines[j]
                    j += 1

                entry = {'名称': name, '丰度%': pct}
                if normal_range:
                    entry['正常范围%'] = normal_range
                if pop_level:
                    entry['人群水平%'] = pop_level
                if detection_rate:
                    entry['检出率%'] = detection_rate
                if desc:
                    entry['说明'] = desc
                results.append(entry)
                i = j
            else:
                i += 1
    else:
        # inline 格式
        sample = region[:500]
        truly_compressed = bool(re.search(r'[a-z]\d', sample, re.IGNORECASE))
        if not truly_compressed:
            # 有空格分隔的inline格式，使用re.finditer
            region_clean = region
            for hdr in ['名称', '丰度%', '正常范围%', '处于人群%水平', '%正常人有检出',
                        '人群水平%', '%人检出']:
                region_clean = region_clean.replace(hdr, '')
            region_clean = re.sub(
                r'说明：[\u4e00-\u9fff\s，。、；：,.;:()（）、/a-zA-Z0-9\-]{10,}?(?=[\u4e00-\u9fff]|$)',
                '', region_clean)
            # 扫描所有匹配的数据行
            for m in re.finditer(
                    r'([\u4e00-\u9fff]{2,12}(?:[（(][\u4e00-\u9fff\w]+[)）])?)\s+'  # 中文名
                    r'(?:[A-Z][a-z]+(?:\s[A-Z][a-z]+)*\s+)?'  # 可选英文名
                    r'(ND|[\d]+\.?[\d]*%?)\s+'  # 丰度
                    r'([\d]+\.?[\d]*-[\d]+\.?[\d]*)?\s*'  # 可选正常范围
                    r'(\d+\.?\d*%?)\s+'  # 人群水平%
                    r'(\d+\.?\d*%)',  # 检出率%
                    region_clean):
                name = m.group(1).strip()
                pct = m.group(2)
                if '病原菌' in name or '构成表' in name or '说明' in name or len(name) <= 1:
                    continue
                normal_range = m.group(3) or ''
                pop_level = m.group(4)
                if not pop_level.endswith('%'):
                    pop_level += '%'
                detection_rate = m.group(5)
                entry = {'名称': name, '丰度%': pct}
                if normal_range:
                    entry['正常范围%'] = normal_range
                entry['人群水平%'] = pop_level
                entry['检出率%'] = detection_rate
                results.append(entry)
            # 模式1没有匹配时：仅中文名+丰度+人群水平(+检出率)
            if not results:
                for m in re.finditer(
                        r'([\u4e00-\u9fff]{2,10}[\u4e00-\u9fff]?)\s+'
                        r'(ND|[\d]+\.?[\d]*%?)\s+'
                        r'(\d+\.?\d*%)\s+'
                        r'(\d+\.?\d*%)?',
                        region_clean):
                    name = m.group(1).strip()
                    pct = m.group(2)
                    if '病原菌' in name or '构成表' in name or '说明' in name or len(name) <= 1:
                        continue
                    pop_level = m.group(3)
                    detection_rate = m.group(4) or ''
                    entry = {'名称': name, '丰度%': pct, '人群水平%': pop_level}
                    if detection_rate:
                        entry['检出率%'] = detection_rate
                    results.append(entry)

    return results


def _parse_phylum_tables(reader, full_text, fmt, title_list=None):
    """提取菌群层级构成表（门/纲/目/科/属/种 level）（移植自 extract_full_report_v5.py）"""
    if title_list is None:
        title_list = PHYLUM_TABLE_TITLES
    results = []
    for phylum_title in title_list:
        rows = _parse_bacteria_table(reader, None, full_text, phylum_title, fmt)
        results.extend(rows)
    return results


def _parse_taxonomy_levels(reader, full_text, fmt):
    """从"菌群检出详细列表"中提取纲目科属种各级数据（移植自 extract_full_report_v5.py）"""
    results = {}
    sidx = full_text.find('菌群检出详细列表')
    if sidx == -1:
        return results

    end_pos = len(full_text)
    for t in ['个体化食物推荐表', '报告总结', '健康总分']:
        ei = full_text.find(t, sidx)
        if ei != -1 and ei < end_pos:
            end_pos = ei

    section = full_text[sidx:end_pos]

    for level, level_name in [('纲', '菌纲构成'), ('目', '菌目构成'),
                              ('科', '菌科构成'), ('属', '菌属构成'),
                              ('种', '菌种构成')]:
        marker = f'\n{level}\n名称\n丰度%'
        marker2 = f'{level} 名称 丰度%'
        li = section.find(marker)
        level_start = None
        if li == -1:
            li2 = section.find(marker2)
            if li2 != -1:
                li = li2
                level_start = li2 + len(marker2)
            else:
                compressed_marker = f'{level}名称丰度%人群水平%%人检出'
                cli = section.find(compressed_marker)
                if cli == -1:
                    continue
                # 压缩格式解析：用正则提取数据
                level_start = cli + len(compressed_marker)
                level_end = len(section)
                for next_level in ['目', '科', '属', '种']:
                    if next_level == level:
                        continue
                    ni = section.find(f'{next_level}名称丰度%人群水平%%人检出', level_start)
                    if ni != -1 and ni < level_end:
                        level_end = ni
                        break
                level_region = section[level_start:level_end]
                compressed_pattern = re.compile(
                    r'([\u4e00-\u9fff·]+(?:\s[\u4e00-\u9fff·]+)?\s+)?'  # 可选中文名
                    r'([A-Za-z][A-Za-z\s.\-]*?)'  # 拉丁名（可能含空格）
                    r'(\d+\.?\d*%)(\d+\.?\d*%)(\d+\.?\d*%)'  # 三连百分比
                )
                rows = []
                for m in compressed_pattern.finditer(level_region):
                    cn_name = (m.group(1) or '').strip()
                    latin_name = m.group(2).strip()
                    pct = m.group(3)
                    pop_level = m.group(4)
                    detection = m.group(5)
                    name = cn_name if cn_name else latin_name
                    entry = {'名称': name, '丰度%': pct, '人群水平%': pop_level, '检出率%': detection}
                    rows.append(entry)
                if rows:
                    results[level_name] = rows
                continue
        else:
            level_start = li + len(marker)

        level_end = len(section)
        for next_level in ['纲', '目', '科', '属', '种']:
            if next_level == level:
                continue
            ni = section.find(f'\n{next_level}\n名称', level_start)
            if ni != -1 and ni < level_end:
                level_end = ni
                break

        level_region = section[level_start:level_end]
        lines = [l.strip() for l in level_region.split('\n') if l.strip()]
        rows = []
        i = 0
        while i < len(lines):
            if lines[i] in ['名称', '丰度%', '人群水平%', '%人检出']:
                i += 1
                continue
            name = lines[i]
            if i + 2 < len(lines) and re.match(r'^[\d]+\.?[\d]*%?$', lines[i + 1]):
                pct = lines[i + 1]
                pop_level = lines[i + 2] if i + 2 < len(lines) else ''
                detection = lines[i + 3] if i + 3 < len(lines) and re.match(r'^[\d.]+%$', lines[i + 3]) else ''
                entry = {'名称': name, '丰度%': pct, '人群水平%': pop_level}
                if detection:
                    entry['检出率%'] = detection
                rows.append(entry)
                i += 4 if detection else 3
            else:
                i += 1

        if rows:
            results[level_name] = rows

    return results


def _extract_bacteria_tables(pdf_path):
    """提取菌群检出详细列表，返回 {中文分组名: [行]}（移植自 extract_full_report_v5.py）

    与原始脚本保持一致的文本构造与格式检测：full_text 使用
    '\\n'.join(norm(p.extract_text()) for p in reader.pages)（不 strip、不过滤空行），
    fmt 使用原脚本 L672-683 的独立检测逻辑。
    """
    reader = PdfReader(pdf_path)
    full_text = '\n'.join(norm(p.extract_text()) for p in reader.pages)

    # 原脚本 extract_bacteria_tables 的格式检测（L674-683）
    fmt = 'triplet' if '指标范围' in full_text and '疾病风险评估' in full_text else 'inline'
    for pt in [p.extract_text() for p in reader.pages]:
        t = norm(pt)
        if '疾病风险评估' in t and '指标范围' in t:
            for line in t.split('\n'):
                if re.search(r'[\u4e00-\u9fff]+\d+\.?\d*[\u4e00-\u9fff]+', line.strip()):
                    fmt = 'inline'
                    break
            break

    all_tables = {}

    # 核心菌属构成表1-3
    core_genus = []
    for i in range(1, 4):
        title = f'核心菌属构成表{i}'
        rows = _parse_bacteria_table(reader, None, full_text, title, fmt)
        core_genus.extend(rows)
    all_tables['核心菌属'] = core_genus

    # 益生菌（使用更精确的表头定位，跳过前面的说明文字）
    prob_marker = '仅列出丰度前22的益生菌种'
    prob_sidx = full_text.find(prob_marker)
    if prob_sidx != -1:
        prob_rows = _parse_bacteria_table(reader, None, full_text, prob_marker, fmt, skip_header=True)
    else:
        prob_rows = _parse_bacteria_table(reader, None, full_text, '益生菌', fmt, skip_header=True)
    all_tables['益生菌'] = [r for r in prob_rows if r.get('名称') and r['名称'] not in
                            ['我的益生菌都为ND', '仅列出丰度前22的益生菌种。']]

    # 有害菌属构成表1-2
    harmful = []
    for i in range(1, 3):
        title = f'有害菌属构成表{i}'
        rows = _parse_bacteria_table(reader, None, full_text, title, fmt)
        harmful.extend(rows)
    all_tables['有害菌属'] = harmful

    # 其它重要菌属
    other_rows = _parse_bacteria_table(reader, None, full_text, '其它重要菌属构成表', fmt)
    all_tables['其它重要菌属'] = other_rows

    # 病原菌属构成表
    patho_genus = _parse_bacteria_table(reader, None, full_text, '病原菌属构成表', fmt)
    all_tables['病原菌属'] = patho_genus

    # 病原菌（检出列表）
    patho_rows = _parse_bacteria_table(reader, None, full_text, '病原菌', fmt, skip_header=True)
    all_tables['病原菌检出'] = [r for r in patho_rows if r.get('名称') and len(r['名称']) >= 2
                               and '仅列出' not in r['名称'] and '说明' not in r['名称']]

    # 菌门构成表（phylum level）
    phylum_rows = _parse_phylum_tables(reader, full_text, fmt)
    if phylum_rows:
        all_tables['菌门构成'] = phylum_rows

    # 菌纲构成表
    class_rows = _parse_phylum_tables(reader, full_text, fmt, CLASS_TABLE_TITLES)
    if class_rows:
        all_tables['菌纲构成'] = class_rows

    # 菌目构成表
    order_rows = _parse_phylum_tables(reader, full_text, fmt, ORDER_TABLE_TITLES)
    if order_rows:
        all_tables['菌目构成'] = order_rows

    # 菌科构成表
    family_rows = _parse_phylum_tables(reader, full_text, fmt, FAMILY_TABLE_TITLES)
    if family_rows:
        all_tables['菌科构成'] = family_rows

    # 菌属构成表
    genus_rows = _parse_phylum_tables(reader, full_text, fmt, GENUS_TABLE_TITLES)
    if genus_rows:
        all_tables['菌属构成'] = genus_rows

    # 菌种构成表
    species_rows = _parse_phylum_tables(reader, full_text, fmt, SPECIES_TABLE_TITLES)
    if species_rows:
        all_tables['菌种构成'] = species_rows

    # 菌群层级（纲目科属种）- 从"菌群检出详细列表"统一入口提取
    taxonomy_rows = _parse_taxonomy_levels(reader, full_text, fmt)
    for key, rows in taxonomy_rows.items():
        if rows:
            all_tables[key] = rows

    return all_tables


def split_7_fields(s):
    """将压缩数字串切分为 7 个字段（移植自 extract_full_report_v5.py）"""
    results = []
    ranges = [(2, 4), (1, 2), (1, 2), (1, 2), (1, 2), (1, 2), (1, 4)]

    def backtrack(pos, idx, nums):
        if idx == 7:
            if pos == len(s):
                results.append(list(nums))
            return
        if pos >= len(s):
            return
        lo, hi = ranges[idx]
        for w in range(lo, min(hi + 1, len(s) - pos + 1)):
            chunk = s[pos:pos + w]
            if chunk.isdigit():
                backtrack(pos + w, idx + 1, nums + [int(chunk)])

    backtrack(0, 0, [])
    return results


def decode_compressed(name, num_str, ref_vals=None):
    """解码压缩食物数字串（移植自 extract_full_report_v5.py）"""
    raw = num_str.lstrip('-')
    has_neg = num_str.startswith('-')
    candidates = []
    for rec_len in range(1, 3):
        if rec_len > len(raw):
            continue
        rec = ('-' if has_neg else '') + raw[:rec_len]
        try:
            rec_val = int(rec)
            if not (-100 <= rec_val <= 100):
                continue
        except Exception:
            continue
        remain = raw[rec_len:]
        for nums in split_7_fields(remain):
            if ref_vals:
                matches = sum(1 for i in range(7) if ref_vals[i] == nums[i])
                if matches >= 6:
                    candidates.append([rec_val] + nums)
            else:
                candidates.append([rec_val] + nums)
    if not candidates:
        return None
    if ref_vals:
        candidates.sort(key=lambda r: (sum(1 for i in range(7) if ref_vals[i] == r[1:][i]),
                                       -len(str(abs(r[0])))), reverse=True)
        if sum(1 for i in range(7) if ref_vals[i] == candidates[0][1:][i]) < 6:
            return None
    else:
        candidates.sort(key=lambda r: (len(str(abs(r[0]))),
                                       -sum(1 for i in range(7) if r[1:][i] == 0)))
    return candidates[0]


def extract_food_table(pdf_path, ref_lookup=None):
    """提取个体化食物推荐表（移植自 extract_full_report_v5.py）"""
    reader = PdfReader(pdf_path)
    food_start = None
    for i, page in enumerate(reader.pages):
        if '个体化食物推荐表' in page.extract_text():
            food_start = i
            break
    if food_start is None:
        return [], 'not_found'

    first_text = norm(reader.pages[food_start + 1].extract_text())
    lines = [l.strip() for l in first_text.split('\n')
             if l.strip() and not re.match(r'\d+/\d+', l)]
    # 判断压缩格式：任何一行超过100字符（单行密集格式），或前10行中超过3行长行
    is_compressed = (len(lines) >= 1 and any(len(l) > 100 for l in lines[:10])) or \
                    sum(1 for l in lines[:10] if len(l) > 100) >= 2

    rows = []
    if is_compressed:
        fmt = 'compressed'
        for i in range(food_start + 1, len(reader.pages)):
            text = norm(reader.pages[i].extract_text())
            text = re.sub(r'\d+/\d+', '', text)
            header = '名称分类推荐指数能量KJ蛋白g脂肪g碳水化合物g淀粉g总膳食纤维g胆固醇mg'
            text = text.replace(header, '')
            for kw in FOOD_SKIP_TEXTS:
                text = text.replace(kw, '')
            while text:
                best_cat, best_idx = None, len(text)
                for cat in KNOWN_CATS:
                    idx = text.find(cat)
                    if idx != -1 and idx < best_idx:
                        best_idx, best_cat = idx, cat
                if best_cat is None:
                    break
                name = text[:best_idx]
                text = text[best_idx + len(best_cat):]
                num_str = ''
                while text and (text[0].isdigit() or text[0] in '-\u2212\u2014'):
                    c = '-' if text[0] in '\u2212\u2014' else text[0]
                    num_str += c
                    text = text[1:]
                if not name or not num_str:
                    continue
                ref_vals = ref_lookup.get(name) if ref_lookup else None
                decoded = decode_compressed(name, num_str, ref_vals)
                if decoded:
                    rows.append(dict(zip(COLUMNS_FOOD, [name, best_cat] + [str(v) for v in decoded])))
    else:
        fmt = 'vertical'
        all_lines = []
        for i in range(food_start + 1, len(reader.pages)):
            for line in norm(reader.pages[i].extract_text()).split('\n'):
                lt = line.strip()
                if not lt or re.match(r'\d+/\d+', lt) or lt in COLUMNS_FOOD:
                    continue
                if len(lt) > 60 and any(k in lt for k in FOOD_SKIP_TEXTS):
                    continue
                all_lines.append(lt)
        i = 0
        while i + 9 < len(all_lines):
            name = all_lines[i].strip()
            cat = all_lines[i + 1].strip()
            if cat not in KNOWN_CATS:
                i += 1
                continue
            nums = []
            ok = True
            for j in range(2, 10):
                v = all_lines[i + j].replace('\u2212', '-').replace('\u2014', '-').strip()
                try:
                    int(v)
                    nums.append(v)
                except Exception:
                    ok = False
                    break
            if ok and len(nums) == 8:
                rows.append(dict(zip(COLUMNS_FOOD, [name, cat] + nums)))
            i += 1
    return rows, fmt


def _extract_food_rows(pdf_path):
    """食物推荐表解析：优先复用同目录其他报告的参考营养表做压缩格式解码"""
    ref_nutrition = {}
    base_dir = os.path.dirname(pdf_path) or '.'
    for fname in sorted(os.listdir(base_dir)):
        if fname.lower().endswith('.pdf') and fname != os.path.basename(pdf_path):
            try:
                tr, _ = extract_food_table(os.path.join(base_dir, fname))
                if len(tr) > 100:
                    for r in tr:
                        ref_nutrition[r['名称']] = [int(r[k]) for k in
                            ['能量KJ', '蛋白g', '脂肪g', '碳水化合物g', '淀粉g',
                             '总膳食纤维g', '胆固醇mg']]
                    break
            except Exception:
                continue
    food_rows, food_fmt = extract_food_table(pdf_path, ref_nutrition or None)
    return food_rows, food_fmt


# ============================================================
# 北京菌群报告 — 指纹检测
# ============================================================

FINGERPRINTS_BEIJING = [
    "肠道微生物健康指数",
    "GMHI",
    "肠道菌群主要检测结果",
    "核心菌属综合评分",
    "有益菌综合评分",
    "有害菌综合评分",
    "肠道菌群精准分布",
    "营养物质及营养素代谢评估",
    "趣味肠菌评估",
    "高通量测序",
]


def detect_beijing_format(text):
    """检测是否为北京菌群报告格式"""
    beijing_matches = sum(1 for f in FINGERPRINTS_BEIJING if f in text)
    if beijing_matches >= 3:
        return True
    return False


# ============================================================
# 北京菌群报告 — 章节提取（PyPDF2 版）
# ============================================================

# 疾病风险关键词（北京报告特有）
DISEASE_KEYWORDS_BJ = [
    "溃疡性结肠炎", "克罗恩病", "腹泻型肠易激综合征",
    "硬化性胆管炎", "非酒精性脂肪性肝病", "肝硬化",
    "便秘", "IgA肾病", "肾结石", "格雷夫斯病",
    "慢性淋巴细胞性甲状腺炎", "强直性脊柱炎",
    "精神分裂症", "痛经",
    "结直肠癌", "胃癌", "甲状腺癌", "肺癌", "乳腺癌",
    "高血压", "冠心病", "2型糖尿病", "高脂血症",
    "食管癌", "胆结石", "哮喘", "心脏病",
    "膜性肾病", "帕金森病", "类风湿关节炎",
]

# 抗生素分类（北京报告格式）
ANTIBIOTIC_CATEGORIES_BJ = [
    "β内酰胺类", "氨基糖苷类", "大环内酯类", "四环素类",
    "氯霉素类", "磺酰胺类", "喹诺酮类", "万古霉素类",
    "头孢菌素类", "磷霉素类", "甲氧苄氨嘧啶类",
    "N-乙酰基转移酶类", "O-磷酸转移酶类", "16S甲基转移酶",
]

# 核心菌属 22 种（北京报告）
CORE_GENERA_BJ = [
    ("阿克曼菌属", "Akkermansia"), ("另枝菌属", "Alistipes"),
    ("拟杆菌属", "Bacteroides"), ("双歧杆菌属", "Bifidobacterium"),
    ("布劳特氏菌属", "Blautia"), ("梭菌属", "Clostridium"),
    ("粪球菌属", "Coprococcus"), ("戴阿利斯特杆菌属", "Dialister"),
    ("多尔氏菌属", "Dorea"), ("真杆菌属", "Eubacterium"),
    ("粪杆菌属", "Faecalibacterium"), ("Lachnoclostridium属", "Lachnoclostridium"),
    ("毛螺菌属", "Lachnospira"), ("乳杆菌属", "Lactobacillus"),
    ("巨单胞菌属", "Megamonas"), ("颤螺旋菌属", "Oscillospira"),
    ("副拟杆菌属", "Parabacteroides"), ("考拉杆菌属", "Phascolarctobacterium"),
    ("普雷沃氏菌属", "Prevotella"), ("罗氏菌属", "Roseburia"),
    ("瘤胃球菌属", "Ruminococcus"), ("萨特氏菌属", "Sutterella"),
]

# 病原体列表（北京报告）
PATHOGEN_LIST_BJ = [
    "气单胞菌属", "蜡样芽孢杆菌", "唐菖蒲伯克霍尔德氏菌",
    "弯曲杆菌属", "艰难梭菌", "肉毒梭菌", "产气荚膜梭菌",
    "幽门螺杆菌", "肺炎克雷伯菌", "类志贺邻单胞菌",
    "沙门氏菌属", "志贺氏菌属", "金黄色葡萄球菌",
    "肺炎链球菌", "霍乱弧菌", "拟态弧菌", "副溶血弧菌",
    "小肠结肠炎耶尔森氏菌", "假结核耶尔森氏菌",
]


def _find_content_after_toc(text):
    """找到北京报告中 TOC 之后的内容起始位置"""
    # 找"第一部分 健康整体评估"后的内容，或者"健康整体评估"正文
    markers = ['第一部分 健康整体评估', '菌群得分总览', '您属于肠']
    for m in markers:
        idx = text.find(m)
        if idx != -1:
            return idx
    return 0


def _find_last_section(text, section_title):
    """找到章节标题的最后一次出现（实际内容，非目录）"""
    last = -1
    start = 0
    while True:
        idx = text.find(section_title, start)
        if idx == -1:
            break
        last = idx
        start = idx + 1
    return last


def _parse_bj_gmhi(text):
    """提取 GMHI 肠道微生物健康指数（从内容区提取）"""
    gmhi = {}
    # 找最后一次出现的 GMHI 值（内容区，非目录）
    content_start = _find_content_after_toc(text)
    content = text[content_start:]

    m = re.search(r'GMHI[）\)]?[为是](\d+)', content)
    if m: gmhi['GMHI'] = float(m.group(1))
    m = re.search(r'肠道微生物健康指数[为](\d+)', content)
    if m: gmhi['肠道微生物健康指数'] = float(m.group(1))
    m = re.search(r'肠道菌群状态[为：:\s]*(\S+?)[。，\n]', content)
    if m: gmhi['肠道菌群状态'] = m.group(1)

    # 健康状态推断
    if gmhi.get('肠道微生物健康指数') or gmhi.get('GMHI'):
        score = gmhi.get('肠道微生物健康指数') or gmhi.get('GMHI', 0)
        if score >= 90: gmhi['健康状态'] = '健康'
        elif score >= 80: gmhi['健康状态'] = '健康倾向'
        elif score >= 40: gmhi['健康状态'] = '亚健康'
        elif score >= 20: gmhi['健康状态'] = '不健康倾向'
        else: gmhi['健康状态'] = '不健康'
    return gmhi


def _parse_bj_gut_type(text):
    """提取肠型"""
    content_start = _find_content_after_toc(text)
    content = text[content_start:]
    m = re.search(r'属于\s*肠[型道]\s*([IVX]+)', content)
    if m: return f'肠型{m.group(1)}'
    m = re.search(r'属于\s*肠[型道]\s*(\S+?)[，。,.\n]', content)
    if m: return m.group(1).strip()
    return None


def _parse_bj_balance(text):
    """提取肠道菌群平衡评估"""
    m = re.search(r'(I{1,3}度失衡)', text)
    if m: return m.group(1)
    return None


def _parse_bj_barrier(text):
    """提取肠道黏膜屏障/BE比值"""
    barrier = {}
    # 在内容区找表格
    content_start = _find_content_after_toc(text)
    content = text[content_start:]
    # 找 BE比值 表格行
    m = re.search(r'BE比[值例][：:\s]*(\d+\.?\d*)', text)
    if m: barrier['BE比值'] = float(m.group(1))
    m = re.search(r'双歧杆菌[属菌][：:\s]*(\d+\.?\d*)', text)
    if m: barrier['双歧杆菌属'] = float(m.group(1))
    m = re.search(r'肠杆菌[科属][：:\s]*(\d+\.?\d*)', text)
    if m: barrier['肠杆菌科'] = float(m.group(1))
    # 综合评估在"BE比值"附近找
    be_idx = content.find('BE比')
    if be_idx != -1:
        chunk = content[be_idx:be_idx + 300]
        m = re.search(r'(正常|轻度损伤|中度损伤|重度损伤|损伤)', chunk)
        if m: barrier['综合评估'] = m.group(1)
    return barrier


def _parse_bj_diversity(text):
    """提取菌群多样性"""
    div = {}
    content_start = _find_content_after_toc(text)
    content = text[content_start:]
    m = re.search(r'多样性指数[为](\d+\.?\d*)', content)
    if m: div['Shannon指数'] = float(m.group(1))
    m = re.search(r'高于[：:\s]*(\d+)%', content)
    if m: div['人群百分位'] = f'高于{m.group(1)}%'
    m = re.search(r'菌种总数[：:\s]*(\d+)', content)
    if m: div['菌种总数'] = int(m.group(1))
    return div


def _parse_bj_phenotype(text):
    """提取菌群表型评估"""
    pheno = {}
    # 找表型评估表格区域
    last_idx = _find_last_section(text, '菌群表型评估')
    if last_idx == -1:
        last_idx = _find_last_section(text, '肠道菌群表型评估')
    if last_idx == -1:
        return pheno
    # 取表格区域
    region = text[last_idx:last_idx + 1500]
    # 解析表格行: 指标名 评估值 结果
    for label, kw in [('革兰氏阳性菌', '阳性菌'), ('革兰氏阴性菌', '阴性菌'),
                       ('生物膜合成', '生物膜'), ('好氧菌', '好氧'),
                       ('厌氧菌', '厌氧'), ('兼性厌氧菌', '兼性'),
                       ('氧化胁迫耐受', '氧化'), ('致病潜力', '致病')]:
        # 找该行: 值在指标名附近
        idx = region.find(kw)
        if idx == -1:
            continue
        chunk = region[idx:idx + 100]
        val_m = re.search(r'(\d+\.?\d*)', chunk)
        if val_m:
            entry = {'评估值': float(val_m.group(1))}
            for status in ['正常', '异常']:
                if status in chunk:
                    entry['结果'] = status
                    break
            pheno[label] = entry
    return pheno


def _parse_bj_scfa(text):
    """提取短链脂肪酸合成能力"""
    scfa = {}
    # 找 SCFA 表格区域（最后一次出现）
    last_idx = _find_last_section(text, '短链脂肪酸合成能力')
    if last_idx == -1:
        last_idx = _find_last_section(text, '短链脂肪酸')
    if last_idx == -1:
        return scfa
    region = text[last_idx:last_idx + 800]
    for acid in ['甲酸', '乙酸', '丙酸', '丁酸', '戊酸', '己酸']:
        m = re.search(rf'{acid}[^a-zA-Z]*?(\d+)', region)
        if m:
            scfa[acid] = int(m.group(1))
    return scfa


def _parse_bj_core_bacteria(text):
    """提取核心菌属精准分布"""
    bacteria = []
    for cn_name, lat_name in CORE_GENERA_BJ:
        idx = text.find(lat_name)
        if idx == -1: idx = text.find(cn_name)
        if idx == -1: continue
        chunk = text[max(0, idx - 50):idx + 200]
        val_m = re.search(r'(\d+\.?\d*)', chunk)
        status_m = re.search(r'(缺失|严重超标|超标|偏低|正常)', chunk)
        pct_m = re.search(r'(\d+\.?\d*)%', chunk)
        range_m = re.search(r'([\d.]+-[\d.]+)', chunk)
        entry = {
            '拉丁名': lat_name,
            '中文名': cn_name,
            '检测结果': float(val_m.group(1)) if val_m else None,
            '状态': status_m.group(1) if status_m else '未知',
            '人群百分位': float(pct_m.group(1)) if pct_m else None,
            '参考范围': range_m.group(1) if range_m else None,
        }
        bacteria.append(entry)
    return bacteria


def _parse_bj_disease_risks(text):
    """提取疾病风险评估"""
    diseases = []
    for keyword in DISEASE_KEYWORDS_BJ:
        idx = text.find(keyword)
        if idx == -1: continue
        chunk = text[idx:idx + 200]
        val_m = re.search(r'(\d+\.\d+)', chunk)
        level_m = re.search(r'(低风险|较低风险|中度风险|较高风险|高风险)', chunk)
        if val_m:
            diseases.append({
                '疾病': keyword,
                '风险指数': float(val_m.group(1)),
                '风险等级': level_m.group(1) if level_m else '',
            })
    return diseases


def _parse_bj_nutrient_metabolism(text):
    """提取营养物质及营养素代谢评估"""
    metabolism = {}
    # 主要营养物质
    for n in ['碳水化合物', '蛋白质', '脂肪', '矿物质']:
        m = re.search(rf'{n}[^估]*?(\d+)', text)
        if m:
            metabolism.setdefault('主要营养物质代谢', {})[n] = int(m.group(1))
    # 糖类
    for item in ['葡萄糖（糖酵解途径）', '葡萄糖（磷酸戊糖途径）', '果糖和甘露糖',
                 '半乳糖', '淀粉和蔗糖', '氨基糖和核苷酸糖', '丙酮酸']:
        m = re.search(rf'{item[:4]}.*?(\d+)', text)
        if m:
            metabolism.setdefault('糖类代谢', {})[item] = int(m.group(1))
    # 脂类
    for item in ['甘油酯', '甘油磷脂', '甘油三酯', '鞘脂类', '脂肪酸',
                 '硬脂酸', '棕榈酸', '花生四烯酸', '二十二碳六烯酸',
                 'Omega-3', 'Omega-6']:
        m = re.search(rf'{item}.*?(\d+)', text)
        if m:
            metabolism.setdefault('脂类代谢', {})[item] = int(m.group(1))
    # 维生素
    for item in ['维生素A', '维生素B1', '维生素B2', '维生素B3', '维生素B5',
                 '维生素B6', '维生素B7', '维生素B12', '维生素C', '维生素D',
                 '维生素E', '维生素K1', '维生素K2', '维生素K3', '叶酸']:
        m = re.search(rf'{item}.*?(\d+)', text)
        if m:
            metabolism.setdefault('维生素', {})[item] = int(m.group(1))
    # 微量元素
    for item in ['铁', '锌', '钙', '镁', '硒', '锰', '铜', '钴', '镍', '钼', '铬', '钒']:
        m = re.search(rf'{item}[^估]*?(\d+)', text)
        if m:
            metabolism.setdefault('微量元素', {})[item] = int(m.group(1))
    # 氨基酸
    for item in ['赖氨酸', '丝氨酸', '亮氨酸', '色氨酸', '苯丙氨酸',
                 '缬氨酸', '组氨酸', '半胱氨酸', '酪氨酸', '丙氨酸',
                 '脯氨酸', '苏氨酸', '谷氨酸', '异亮氨酸', '精氨酸',
                 '蛋氨酸', '甘氨酸', '天冬氨酸', '牛磺酸']:
        m = re.search(rf'{item}[^估]*?(\d+)', text)
        if m:
            metabolism.setdefault('氨基酸', {})[item] = int(m.group(1))
    # 神经递质
    for item in ['5-羟色胺', 'γ-氨基丁酸', '多巴胺', '乙酰胆碱', '组胺', '去甲肾上腺素']:
        m = re.search(rf'{item}.*?(\d+)', text)
        if m:
            metabolism.setdefault('神经递质', {})[item] = int(m.group(1))
    # 其他单项
    for pattern, key in [
        (r'嘌呤代谢.*?(\d+)', '嘌呤代谢'),
        (r'谷胱甘肽.*?(\d+)', '三肽（谷胱甘肽）'),
        (r'胆汁酸.*?(\d+)', '胆汁酸代谢'),
        (r'硫辛酸.*?(\d+)', '抗自由基（硫辛酸）'),
        (r'辅酶Q.*?(\d+)', '抗自由基（辅酶Q）'),
    ]:
        m = re.search(pattern, text)
        if m:
            metabolism[key] = int(m.group(1))
    return metabolism


def _parse_bj_antibiotics(text):
    """提取抗生素风险评估"""
    ab = {}
    for cat in ANTIBIOTIC_CATEGORIES_BJ:
        m = re.search(rf'{cat}[：:\s]*(\d+)', text)
        if m:
            ab[cat] = int(m.group(1))
    return ab


def _parse_bj_toxins(text):
    """提取毒性物质清除能力评估"""
    toxins = {}
    toxin_items = [
        "苯甲酸酯", "对氨基苯甲酸乙酯", "对氟苯甲酸乙酯",
        "氯烷烃和氯烯烃", "氯代环己烷", "氯苯",
        "甲苯", "二甲苯", "硝基甲苯", "乙苯", "苯乙烯",
        "阿特拉津", "己内酰胺", "双酚", "二恶英",
        "萘", "多环芳烃",
    ]
    for item in toxin_items:
        m = re.search(rf'{item}.*?(\d+)', text)
        if m:
            toxins[item] = int(m.group(1))
    return toxins


def _parse_bj_pathogens(text):
    """提取胃肠道感染病原体评估"""
    pathogens = []
    for p in PATHOGEN_LIST_BJ:
        idx = text.find(p)
        if idx == -1: continue
        chunk = text[idx:idx + 150]
        val_m = re.search(r'(\d+\.?\d*)', chunk)
        status_m = re.search(r'(检出|超标|未检出|正常)', chunk)
        if val_m:
            entry = {'名称': p, '检测值': float(val_m.group(1)) if '.' in val_m.group(1) else int(val_m.group(1))}
            if status_m: entry['状态'] = status_m.group(1)
            pathogens.append(entry)
    return pathogens


def _parse_bj_psych_eval(text, find_table_val=None):
    """提取趣味肠菌评估"""
    psych = {}
    m = re.search(r'最高概率[：:\s]*(\S+)', text)
    if m: psych['人格特征'] = {'最高概率': m.group(1)}
    # 认知功能（从表格）
    if find_table_val:
        cog = find_table_val('认知能力', val_col=1)
        if cog:
            psych['认知功能'] = {'认知能力评分': int(cog)}
    return psych


def _parse_bj_scfa_from_tables(find_table_rows):
    """从表格提取短链脂肪酸合成能力"""
    scfa = {}
    for acid in ['甲酸', '乙酸', '丙酸', '丁酸', '戊酸', '己酸']:
        rows = find_table_rows(acid)
        for name, val in rows:
            if acid in name:
                scfa[acid] = int(val)
                break
    return scfa


def _parse_bj_core_bacteria_from_tables(all_tables):
    """从表格提取核心菌属精准分布"""
    bacteria = []
    for cn_name, lat_name in CORE_GENERA_BJ:
        for table in all_tables:
            for row in table:
                row_str = ' '.join(str(c) for c in row if c)
                if lat_name in row_str or cn_name in row_str:
                    vals = [str(c).strip() for c in row if c and str(c).strip()]
                    entry = {'拉丁名': lat_name, '中文名': cn_name}
                    for v in vals:
                        v_clean = v.replace('"', '').replace('#', '').strip()
                        # 判断是否为范围值（如 0.0041-0.0339）
                        if '-' in v_clean and v_clean.replace('.','').replace('-',' ').replace(' ','').isdigit():
                            entry['参考范围'] = v_clean
                        elif v_clean == 'ND':
                            if '检测结果' not in entry:
                                entry['检测结果'] = 0.0
                        elif v_clean.replace('.','').replace('-','').isdigit() and v_clean != '':
                            val = float(v_clean)
                            if '检测结果' not in entry:
                                entry['检测结果'] = val
                            elif '人群百分位' not in entry:
                                entry['人群百分位'] = val
                    if '检测结果' in entry:
                        bacteria.append(entry)
                    break
            if bacteria and bacteria[-1].get('拉丁名') == lat_name:
                break
    return bacteria


def _parse_bj_nutrient_from_tables(find_table_rows, find_table_val):
    """从表格提取营养物质及营养素代谢评估"""
    metabolism = {}
    # 主要营养物质
    for n in ['碳水化合物', '蛋白质', '脂肪', '矿物质']:
        rows = find_table_rows(n)
        if rows:
            for name, val in rows:
                if n in name:
                    metabolism.setdefault('主要营养物质代谢', {})[n] = int(val)
    # 糖类
    sugar_items = ['葡萄糖（糖酵解途径）', '葡萄糖（磷酸戊糖途径）', '果糖和甘露糖',
                   '半乳糖', '淀粉和蔗糖', '氨基糖和核苷酸糖', '丙酮酸']
    for item in sugar_items:
        rows = find_table_rows(item[:3])
        if rows:
            for name, val in rows:
                metabolism.setdefault('糖类代谢', {})[item] = int(val)
    # 脂类
    for item in ['甘油酯', '甘油磷脂', '甘油三酯', '鞘脂类', '脂肪酸',
                 '硬脂酸', '棕榈酸', '花生四烯酸', '二十二碳六烯酸',
                 'Omega-3', 'Omega-6']:
        rows = find_table_rows(item[:3])
        if rows:
            for name, val in rows:
                metabolism.setdefault('脂类代谢', {})[item] = int(val)
    # 维生素
    for item in ['维生素A', '维生素B1', '维生素B2', '维生素B3', '维生素B5',
                 '维生素B6', '维生素B7', '维生素B12', '维生素C', '维生素D',
                 '维生素E', '维生素K1', '维生素K2', '维生素K3', '叶酸']:
        rows = find_table_rows(item)
        if rows:
            for name, val in rows:
                metabolism.setdefault('维生素', {})[item] = int(val)
    # 微量元素
    for item in ['铁', '锌', '钙', '镁', '硒', '锰', '铜', '钴', '镍', '钼', '铬', '钒']:
        rows = find_table_rows(item)
        if rows:
            for name, val in rows:
                if name == item:
                    metabolism.setdefault('微量元素', {})[item] = int(val)
    # 氨基酸
    for item in ['赖氨酸', '丝氨酸', '亮氨酸', '色氨酸', '苯丙氨酸',
                 '缬氨酸', '组氨酸', '半胱氨酸', '酪氨酸', '丙氨酸',
                 '脯氨酸', '苏氨酸', '谷氨酸', '异亮氨酸', '精氨酸',
                 '蛋氨酸', '甘氨酸', '天冬氨酸', '牛磺酸']:
        rows = find_table_rows(item[:2])
        if rows:
            for name, val in rows:
                metabolism.setdefault('氨基酸', {})[item] = int(val)
    # 神经递质
    for item in ['5-羟色胺', 'γ-氨基丁酸', '多巴胺', '乙酰胆碱', '组胺', '去甲肾上腺素']:
        rows = find_table_rows(item[:3])
        if rows:
            for name, val in rows:
                metabolism.setdefault('神经递质', {})[item] = int(val)
    # 其他单项
    for item, key in [('嘌呤代谢', '嘌呤代谢'), ('谷胱甘肽', '三肽（谷胱甘肽）'),
                       ('胆汁酸', '胆汁酸代谢'), ('硫辛酸', '抗自由基（硫辛酸）'),
                       ('辅酶Q', '抗自由基（辅酶Q）')]:
        v = find_table_val(item)
        if v: metabolism[key] = int(v)
    return metabolism


def _parse_bj_antibiotics_from_tables(find_table_rows):
    """从表格提取抗生素风险评估"""
    ab = {}
    for cat in ANTIBIOTIC_CATEGORIES_BJ:
        rows = find_table_rows(cat, val_col=2)
        for name, val in rows:
            ab[cat] = int(val)
    return ab


def _parse_bj_toxins_from_tables(all_tables, find_table_rows):
    """从表格提取毒性物质清除能力评估"""
    toxins = {}
    toxin_items = [
        "苯甲酸酯", "对氨基苯甲酸乙酯", "对氟苯甲酸乙酯",
        "氯烷烃和氯烯烃", "氯代环己烷", "氯苯",
        "甲苯", "二甲苯", "硝基甲苯", "乙苯", "苯乙烯",
        "阿特拉津", "己内酰胺", "双酚", "二恶英",
        "萘", "多环芳烃",
    ]
    for item in toxin_items:
        rows = find_table_rows(item[:3], name_col=1, val_col=2)
        for name, val in rows:
            toxins[item] = int(val)
    return toxins


def _parse_bj_overview(text):
    """提取北京报告概述（统一到标准报告 overview 结构）"""
    r = {}
    m = re.search(r'检测编号[：:\s]*(\S+)', text)
    if m: r['report_number'] = m.group(1)
    m = re.search(r'姓\s*名[：:\s]*(\S+)', text)
    if m: r['person_name'] = m.group(1)
    m = re.search(r'年\s*龄[：:\s]*(\S+)', text)
    if m: r['age'] = m.group(1)
    m = re.search(r'性\s*别[：:\s]*(\S+)', text)
    if m: r['gender'] = 'male' if m.group(1) in ('男', 'M') else 'female'
    # 肠型
    gut_type = _parse_bj_gut_type(text)
    if gut_type: r['gut_type'] = gut_type
    # GMHI → 健康总分
    m = re.search(r'肠道微生物健康指数[：:\s]*(\d+)', text)
    if m: r['overallScore'] = int(m.group(1))
    return r


def _parse_beijing_report(file_path: str) -> dict:
    """解析北京菌群报告 PDF，输出统一结构（pdfplumber 表格+文本混合提取）"""
    try:
        import pdfplumber
        with pdfplumber.open(file_path) as pdf:
            text = '\n'.join(page.extract_text() or '' for page in pdf.pages)
            # 提取所有表格
            all_tables = []
            for page in pdf.pages:
                tables = page.extract_tables()
                for table in tables:
                    if table and len(table) >= 2:
                        all_tables.append(table)
    except Exception as e:
        from PyPDF2 import PdfReader
        reader = PdfReader(file_path)
        text = '\n'.join((page.extract_text() or '') for page in reader.pages)
        all_tables = []

    def find_table_rows(keyword, val_col=1, name_col=0, try_all=False):
        """从表格中找指定关键词的数据行"""
        rows = []
        for table in all_tables:
            for row in table:
                row_str = ' '.join(str(c) for c in row if c)
                if keyword in row_str:
                    if name_col < len(row) and val_col < len(row):
                        name = str(row[name_col] or '').strip()
                        val = str(row[val_col] or '').strip()
                        if name and val and val.replace('.','').replace('-','').isdigit():
                            rows.append((name, val))
            if rows and not try_all:
                break
        return rows

    def find_table_val(keyword, val_col=1, name_col=0):
        """从表格中找单个值"""
        for table in all_tables:
            for row in table:
                row_str = ' '.join(str(c) for c in row if c)
                if keyword in row_str:
                    if val_col < len(row):
                        val = str(row[val_col] or '').strip()
                        if val and val.replace('.','').isdigit():
                            return val
        return None

    result = {
        'format': 'beijing',
        'overview': _parse_bj_overview(text),
        'disease_risks': [],
        'nutrition': [],
        'amino_acids': [],
        'vitamins': [],
        'trace_elements': [],
        '菌群检出详细列表': {},
        '个体化食物推荐表': {'格式': 'not_found', '条目数': 0, '数据': []},
        # 北京报告特有指标
        '肠道微生物健康指数': _parse_bj_gmhi(text),
        '菌群多样性': _parse_bj_diversity(text),
        '肠道黏膜屏障': _parse_bj_barrier(text),
        '菌群表型评估': _parse_bj_phenotype(text),
        '短链脂肪酸合成能力': _parse_bj_scfa_from_tables(find_table_rows),
        '肠道菌群精准分布': _parse_bj_core_bacteria_from_tables(all_tables),
        '营养物质及营养素代谢评估': _parse_bj_nutrient_from_tables(find_table_rows, find_table_val),
        '抗生素风险评估': _parse_bj_antibiotics_from_tables(find_table_rows),
        '毒性物质清除能力评估': _parse_bj_toxins_from_tables(all_tables, find_table_rows),
        '趣味肠菌评估': _parse_bj_psych_eval(text, find_table_val),
        '胃肠道感染病原体': [],
        '健康整体评估': {},
        '肠道菌群主要检测结果': {},
    }

    # 从表格更新 GMHI/抗炎/免疫/纤维/多样性/屏障
    gmhi_val = find_table_val('肠道微生物健康指数', val_col=1)
    if gmhi_val:
        result['肠道微生物健康指数']['肠道微生物健康指数'] = float(gmhi_val)
        score = float(gmhi_val)
        if score >= 90: result['肠道微生物健康指数']['健康状态'] = '健康'
        elif score >= 80: result['肠道微生物健康指数']['健康状态'] = '健康倾向'
        elif score >= 40: result['肠道微生物健康指数']['健康状态'] = '亚健康'
        elif score >= 20: result['肠道微生物健康指数']['健康状态'] = '不健康倾向'
        else: result['肠道微生物健康指数']['健康状态'] = '不健康'
    for attr, kw in [('肠道抗炎能力', '抗炎能力'), ('肠道免疫力', '免疫力'),
                     ('肠道膳食纤维需求', '膳食纤维需求')]:
        v = find_table_val(kw)
        if v:
            result.setdefault('肠道菌群主要检测结果', {})[attr] = int(v)
            if '抗炎' in kw: result['overview']['inflammationScore'] = int(v)
            elif '免疫' in kw: result['overview']['immunityScore'] = int(v)
    # 多样性
    div_val = find_table_val('肠道微生物多样性', val_col=1)
    if div_val:
        result['菌群多样性']['Shannon指数'] = float(div_val)
    # BE比值
    be_val = find_table_val('B/E比值', val_col=1)
    if be_val:
        result['肠道黏膜屏障']['BE比值'] = float(be_val)
    bi_val = find_table_val('双歧杆菌属', val_col=1)
    if bi_val:
        result['肠道黏膜屏障']['双歧杆菌属'] = float(bi_val)
    ent_val = find_table_val('肠杆菌科', val_col=1)
    if ent_val:
        result['肠道黏膜屏障']['肠杆菌科'] = float(ent_val)
    # 肠型
    gut_type = _parse_bj_gut_type(text)
    balance = _parse_bj_balance(text)
    if gut_type or balance:
        result['健康整体评估'] = {}
        if gut_type: result['健康整体评估']['肠型'] = gut_type
        if balance: result['健康整体评估']['菌群平衡评估'] = balance

    # 疾病风险评估（文本提取）
    disease_risks = _parse_bj_disease_risks(text)
    if disease_risks:
        result['disease_risks'] = disease_risks

    # 病原体
    pathogens = _parse_bj_pathogens(text)
    if pathogens:
        result['胃肠道感染病原体'] = pathogens

    # 营养物质 → 标准字段映射
    metabolism = result.get('营养物质及营养素代谢评估', {})
    if metabolism.get('主要营养物质代谢'):
        result['nutrition'] = [
            {'name': k, 'value': str(v), 'status': '正常' if v >= 60 else '偏低'}
            for k, v in metabolism['主要营养物质代谢'].items()
        ]
    if metabolism.get('氨基酸'):
        result['amino_acids'] = [
            {'name': k, 'value': str(v), 'status': '正常' if v >= 60 else '偏低'}
            for k, v in metabolism['氨基酸'].items()
        ]
    if metabolism.get('维生素'):
        result['vitamins'] = [
            {'name': k, 'value': str(v), 'status': '正常' if v >= 60 else '偏低'}
            for k, v in metabolism['维生素'].items()
        ]
    if metabolism.get('微量元素'):
        result['trace_elements'] = [
            {'name': k, 'value': str(v), 'status': '正常' if v >= 60 else '偏低'}
            for k, v in metabolism['微量元素'].items()
        ]

    return result