在 Python 中解析嵌套和复杂的 XML

Question

我正在尝试解析相当复杂的 xml 文件并将其内容存储在数据框中。我尝试 xml.etree.ElementTree 并设法检索了一些元素，但我以某种方式多次检索它，就好像有更多对象一样。我正在尝试提取以下内容：category, created, last_updated, accession type, name type identifier, name type synonym as a list

<cellosaurus>
<cell-line category="Hybridoma" created="2012-06-06" last_updated="2020-03-12" entry_version="6">
  <accession-list>
    <accession type="primary">CVCL_B375</accession>
  </accession-list>
  <name-list>
    <name type="identifier">#490</name>
    <name type="synonym">490</name>
    <name type="synonym">Mab 7</name>
    <name type="synonym">Mab7</name>
  </name-list>
  <comment-list>
    <comment category="Monoclonal antibody target"> Cronartium ribicola antigens </comment>
    <comment category="Monoclonal antibody isotype"> IgM, kappa </comment>
  </comment-list>
  <species-list>
    <cv-term terminology="NCBI-Taxonomy" accession="10090">Mus musculus</cv-term>
  </species-list>
  <derived-from>
    <cv-term terminology="Cellosaurus" accession="CVCL_4032">P3X63Ag8.653</cv-term>
  </derived-from>
  <reference-list>
    <reference resource-internal-ref="Patent=US5616470"/>
  </reference-list>
  <xref-list>
    <xref database="CLO" category="Ontologies" accession="CLO_0001018">
      <url><![CDATA[https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/CLO_0001018]]></url>
    </xref>
    <xref database="ATCC" category="Cell line collections" accession="HB-12029">
      <url><![CDATA[https://www.atcc.org/Products/All/HB-12029.aspx]]></url>
    </xref>
    <xref database="Wikidata" category="Other" accession="Q54422073">
      <url><![CDATA[https://www.wikidata.org/wiki/Q54422073]]></url>
    </xref>
  </xref-list>
</cell-line>
</cellosaurus>

Answer 1

您的问题有点不清楚，因为在某些情况下您希望解析标签属性，而在其他情况下您希望解析 tag_values。

我的理解如下。您需要以下值：

标签类别属性的值 cell-line.
标签 created 属性的值 cell-line.
标签 cell-line.

last_updated

标签类型的属性值加入。
标签name对应的文本，属性为identifier.
标签name对应的文本，属性为synonym.

可以使用模块 xml.etree.Etree 从 xml 文件中提取这些值。特别是，请查看使用元素 class.

的 findall and iter 方法

假设 xml 在名为 input.xml 的文件中，下面的代码片段应该可以解决问题。

import xml.etree.ElementTree as et


def main():
    tree = et.parse('cellosaurus.xml')
    root = tree.getroot()

    results = []
    for element in root.findall('.//cell-line'):
        key_values = {}
        for key in ['category', 'created', 'last_updated']:
            key_values[key] = element.attrib[key]
        for child in element.iter():
            if child.tag == 'accession':
                key_values['accession type'] = child.attrib['type']
            elif child.tag == 'name' and child.attrib['type'] == 'identifier':
                key_values['name type identifier'] = child.text
            elif child.tag == 'name' and child.attrib['type'] == 'synonym':
                key_values['name type synonym'] = child.text
        results.append([
                # Using the get method of the dict object in case any particular
                # entry does not have all the required attributes.
                 key_values.get('category'            , None)
                ,key_values.get('created'             , None)
                ,key_values.get('last_updated'        , None)
                ,key_values.get('accession type'      , None)
                ,key_values.get('name type identifier', None)
                ,key_values.get('name type synonym'   , None)
                ])

    print(results)


if __name__ == '__main__':
    main()

Answer 2

解析 xml 的最简单方法是，恕我直言，使用 lxml。

from lxml import etree
data = """[your xml above]"""
doc = etree.XML(data)
for att in doc.xpath('//cell-line'):
    print(att.attrib['category'])
    print(att.attrib['last_updated'])
    print(att.xpath('.//accession/@type')[0])
    print(att.xpath('.//name[@type="identifier"]/text()')[0])
    print(att.xpath('.//name[@type="synonym"]/text()'))

输出：

Hybridoma
2020-03-12
primary
#490
['490', 'Mab 7', 'Mab7']

然后您可以将输出分配给变量、附加到列表等。

Answer 3

另一种方法。最近比较了几个XML解析库，发现这个好用。我推荐。

from simplified_scrapy import SimplifiedDoc, utils

xml = '''your xml above'''
# xml = utils.getFileContent('your file name.xml')

results = []
doc = SimplifiedDoc(xml)
for ele in doc.selects('cell-line'):
  key_values = {}
  for k in ele:
    if k not in ['tag','html']:
      key_values[k]=ele[k]
  key_values['name type identifier'] = ele.select('name@type="identifier">text()')
  key_values['name type synonym'] = ele.selects('name@type="synonym">text()')
  results.append(key_values)
print (results)

结果：

[{'category': 'Hybridoma', 'created': '2012-06-06', 'last_updated': '2020-03-12', 'entry_version': '6', 'name type identifier': '#490', 'name type synonym': ['490', 'Mab 7', 'Mab7']}]

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