Python lxml高效查找文本

Question

使用python lxml，我想测试XML文档是否包含EXPERIMENT_TYPE，如果存在，则提取。

示例：

<EXPERIMENT_SET>
  <EXPERIMENT center_name="BCCA" alias="Experiment-pass_2.0">
    <TITLE>WGBS (whole genome bisulfite sequencing) analysis of SomeSampleA (library: SomeLibraryA).</TITLE>
    <STUDY_REF accession="SomeStudy" refcenter="BCCA"/>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE><TAG>EXPERIMENT_TYPE</TAG><VALUE>DNA Methylation</VALUE></EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE><TAG>EXPERIMENT_ONTOLOGY_URI</TAG><VALUE>http://purl.obolibrary.org/obo/OBI_0001863</VALUE></EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE><TAG>EXPERIMENT_ONTOLOGY_CURIE</TAG><VALUE>obi:0001863</VALUE></EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE><TAG>MOLECULE</TAG><VALUE>genomic DNA</VALUE></EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>

有没有比遍历所有元素更快的方法？

    all = etree.findall('EXPERIMENT/EXPERIMENT_ATTRIBUTES/EXPERIMENT_ATTRIBUTE/TAG')
    
    for e in all:
        if e.text == 'EXPERIMENT_TYPE':
            print("Found")

当我想要提取的时候，这种尝试也变得很混乱。

Answer 1

你最好用XPath来做这件事，这肯定是非常快的。我的建议(测试和工作)。它将返回一个(可能为空的) VALUE元素列表，您可以从中获得额外的text。

PS:不要使用诸如all之类的“特殊”字作为变量名。糟糕的实践可能会导致意想不到的错误。

import lxml.etree as ET
from lxml.etree import Element
from typing import List

xml_str = """
<EXPERIMENT_SET>
  <EXPERIMENT center_name="BCCA" alias="Experiment-pass_2.0">
    <TITLE>WGBS (whole genome bisulfite sequencing) analysis of SomeSampleA (library: SomeLibraryA).</TITLE>
    <STUDY_REF accession="SomeStudy" refcenter="BCCA"/>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE><TAG>EXPERIMENT_TYPE</TAG><VALUE>DNA Methylation</VALUE></EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE><TAG>EXPERIMENT_ONTOLOGY_URI</TAG><VALUE>http://purl.obolibrary.org/obo/OBI_0001863</VALUE></EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE><TAG>EXPERIMENT_ONTOLOGY_CURIE</TAG><VALUE>obi:0001863</VALUE></EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE><TAG>MOLECULE</TAG><VALUE>genomic DNA</VALUE></EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>
"""


tree = ET.ElementTree(ET.fromstring(xml_str))
vals: List[Element] = tree.xpath(".//EXPERIMENT_ATTRIBUTE/TAG[text()='EXPERIMENT_TYPE']/following-sibling::VALUE")
print(vals[0].text)
# DNA Methylation

Michael Kay在下面提供了一个替代的XPath声明，该声明与Martin Honnen的答案相同。

.//EXPERIMENT_ATTRIBUTE[TAG='EXPERIMENT_TYPE']/VALUE

Answer 2

就XPath而言，您似乎只需要使用/EXPERIMENT_SET/EXPERIMENT/EXPERIMENT_ATTRIBUTES/EXPERIMENT_ATTRIBUTE[TAG = 'EXPERIMENT_TYPE']/VALUE等标记元素来选择VALUE元素。

我认为在Python和lxml中，人们经常使用文本节点选择，例如/EXPERIMENT_SET/EXPERIMENT/EXPERIMENT_ATTRIBUTES/EXPERIMENT_ATTRIBUTE[TAG = 'EXPERIMENT_TYPE']/VALUE/text()，然后xpath函数将其作为Python字符串返回。

Answer 3

使用findall是一种很自然的方式。我建议使用以下代码来查找这些值：

from lxml import etree

root = etree.parse('toto.xml').getroot()

all = root.findall('EXPERIMENT/EXPERIMENT_ATTRIBUTES/EXPERIMENT_ATTRIBUTE/TAG')
for e in all:
    if e.text == 'EXPERIMENT_TYPE':
        v = e.getparent().find('VALUE')
        if v is not None:
            print(f'Found val="{v.text}"')

这将输出以下内容：

Found val="DNA Methylation"