使用 Python xml.etree.ElementTree 遍历 XML 树的问题

debugcn 发表于 Dev

毛罗比奥

我有一个结构如下所示的 XML 文件（为了这个问题的目的而简化）。对于每条记录，我想提取文章标题和“ArticleId”元素中包含DOI编号的属性“IdType”的值（有时这个属性可能会丢失），然后将文章标题存储在带有DOI的字典中作为关键。

<PubmedArticleSet>
<PubmedArticle>
    <MedlineCitation Status="MEDLINE" Owner="NLM">
        <Article PubModel="Print-Electronic">
            <ArticleTitle>Malathion and dithane induce DNA damage in Vicia faba.</ArticleTitle>
        </Article>
    </MedlineCitation>  
    <PubmedData>
        <ArticleIdList>
            <ArticleId IdType="pubmed">28950791</ArticleId>
            <ArticleId IdType="doi">10.1177/0748233717726877</ArticleId>
        </ArticleIdList>
    </PubmedData>
</PubmedArticle>

<PubmedArticle>
    <MedlineCitation Status="MEDLINE" Owner="NLM">
        <Article PubModel="Print-Electronic">
            <ArticleTitle>Impact of dual inoculation with Rhizobium and PGPR on growth and antioxidant status of Vicia faba L. under copper stress.</ArticleTitle>
        </Article>
    </MedlineCitation>  
    <PubmedData>
        <ArticleIdList>
            <ArticleId IdType="pubmed">25747267</ArticleId>
            <ArticleId IdType="pii">S1631-0691(15)00050-5</ArticleId>
            <ArticleId IdType="doi">10.1016/j.crvi.2015.02.001</ArticleId>
        </ArticleIdList>
    </PubmedData>
</PubmedArticle>

<PubmedArticle>
    <MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM">
        <Article PubModel="Print-Electronic">
            <ArticleTitle>[Influence of Four Kinds of PPCPs on Micronucleus Rate of the Root-Tip Cells of Vicia-faba and Garlic].</ArticleTitle>
        </Article>
    </MedlineCitation>
    <PubmedData>
    <ArticleIdList>
        <ArticleId IdType="pubmed">27548984</ArticleId>
        <!-- in this record, DOI is missing -->
    </ArticleIdList>
    </PubmedData>
</PubmedArticle>
</PubmedArticleSet>

为了实现这一点，我使用了 xml.etree.ElementTree，如下所示：

import xml.etree.ElementTree as ET

xmldoc = ET.parse('sample.xml')
root = xmldoc.getroot()
pubs = {}
for elem in xmldoc.iter(tag='ArticleTitle'):
    title = elem.text
    for subelem in xmldoc.iter(tag='ArticleId'):
        if subelem.get("IdType") == "doi":
            doi = subelem.text 
            pubs[doi] = title

if len(pubs) == 0:
   print "No articles found"
else:   
   for pub in pubs.keys():
       print pub + ' ' + pubs[pub]

但是遍历文档树的循环有问题，因为上面的代码导致：

10.1177/0748233717726877 [Influence of Four Kinds of PPCPs on Micronucleus Rate of the Root-Tip Cells of Vicia-faba and Garlic].
10.1016/j.crvi.2015.02.001 [Influence of Four Kinds of PPCPs on Micronucleus Rate of the Root-Tip Cells of Vicia-faba and Garlic].

也就是说，我得到了正确的 DOI，但只是上一篇文章标题的副本，没有 DOI！

正确的输出应该是：

10.1177/0748233717726877 Malathion and dithane induce DNA damage in Vicia faba.
10.1016/j.crvi.2015.02.001 Impact of dual inoculation with Rhizobium and PGPR on growth and antioxidant status of Vicia faba L. under copper stress.

任何人都可以向我提供一些解决这个烦人问题的提示吗？

托马拉克

这从根本上是错误的：

for elem in xmldoc.iter(tag='ArticleTitle'):      # <-- *ALL* <ArticleTitle> elements
    ...
    for subelem in xmldoc.iter(tag='ArticleId'):  # <-- *ALL* <ArticleId> elements
        ...

在 ElementTree 中没有读心术，它只选择与您<ArticleId>最后一次看到的相关联的内容<ArticleTitle>，因此您找到的任何与该代码相关的内容实际上都不会相关。

围绕实际的 XML 文档构建您的代码（“for each PubmedArticle...”）并使用相对搜索：

pubs = []

for pubmedArticle in xmldoc.iter(tag='PubmedArticle'):  
    # relative search within this <PubmedArticle>
    articleTitle = pubmedArticle.find('./MedlineCitation/Article/ArticleTitle')

    # always verify that there are actual results for a search
    if articleTitle == None:
       title = "No article title found"
    else:
       title = articleTitle.text

    for articleId in pubmedArticle.iterfind('./PubmedData//ArticleId'):
        if articleId.get("IdType") == "doi":
            pubs.append({"doi": articleId.text, "title": title})

我还建议制作一个字典列表，而不是单个字典。在您的以下代码中处理会更容易：

[
    {'doi': '10.1177/0748233717726877', 'title': 'Malathion and dithane induce DNA damage in Vicia faba.'},
    {'doi': '10.1016/j.crvi.2015.02.001', 'title': 'Impact of dual inoculation with Rhizobium and PGPR on growth and antioxidant status of Vicia faba L. under copper stress.'}
]

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