Python中用lxml获取XML指定元素文本报错的解决方法

问题场景 #

给定以下XML片段：

<root>
   <doc>
      <field name="id">metadata_9606_SAMN03465421</field>
      <field name="is_metadata">true</field>
      <field name="is_sample">true</field>
      <field name="project_desc">PRJNA280600</field>
      <field name="taxid">9606</field>
      <field name="source_name">uterus</field>
      <field name="sample_id">SAMN03465421</field>
      <field name="exp_Mcount">13341.1</field>
   </doc>
   <doc>
      <field name="id">1_SAMN03465421</field>
      <field name="gene">1</field>
      <field name="sample_id">SAMN03465421</field>
<field name="source_name">uterus</field><field name="var">0</field>
      <field name="full_rpkm">0.133911</field>
      <field name="exp_rpkm">0.134</field>
      <field name="exp_total">3155</field>
      <field name="project_desc">PRJNA280600</field>
   </doc>
   <doc>
      <field name="id">1_SAMN03465420</field>
      <field name="gene">1</field>
      <field name="sample_id">SAMN03465420</field>
<field name="source_name">trachea</field><field name="var">0</field>
      <field name="full_rpkm">0.0232912</field>
      <field name="exp_rpkm">0.0233</field>
      <field name="exp_total">604</field>
      <field name="project_desc">PRJNA280600</field>
   </doc>
</root>

用户尝试用以下代码查找每个<doc>下name属性为source_name的<field>元素文本：

import lxml.etree
tree = lxml.etree.parse(<PATH TO DOCUMENT>)
root = tree.getroot()
print(root.findall('/doc/field name[4]'))

运行后出现错误：

Traceback (most recent call last):
  File "/home/alex/PycharmProjects/gene_expression_ftp/main.py", line 4, in <module>
    print(root.findall('/doc/field name[4]'))
  File "src/lxml/etree.pyx", line 1575, in lxml.etree._Element.findall
  File "src/lxml/_elementpath.py", line 334, in lxml._elementpath.findall
  File "src/lxml/_elementpath.py", line 312, in lxml._elementpath.iterfind
  File "src/lxml/_elementpath.py", line 281, in lxml._elementpath._build_path_iterator
SyntaxError: cannot use absolute path on element

错误原因 #

1. 绝对路径使用错误：root已经是<root>元素，使用/doc会被当作绝对路径（从文档根开始），而非相对于root的路径，触发语法错误。
2. XPath属性筛选语法错误：筛选name属性为source_name的元素，正确语法是field[@name='source_name']，而非field name[4]。

正确实现方式 #

方式一：使用正确的相对XPath #

import lxml.etree

tree = lxml.etree.parse("<PATH TO DOCUMENT>")
root = tree.getroot()

# 查找所有doc下name为source_name的field元素
source_fields = root.findall("./doc/field[@name='source_name']")

# 遍历并打印每个元素的文本
for field in source_fields:
    print(field.text)

方式二：遍历每个doc元素再查找目标field #

如果需要同时获取doc下其他关联信息，这种方式更灵活：

import lxml.etree

tree = lxml.etree.parse("<PATH TO DOCUMENT>")
root = tree.getroot()

for doc in root.findall("./doc"):
    # 在当前doc下查找目标field
    source_field = doc.find("./field[@name='source_name']")
    if source_field is not None:
        print(source_field.text)

运行以上代码会输出：

uterus
uterus
trachea

内容的提问来源于stack exchange，提问作者user18544188