如何提取 XML 特定的值字段并列出它们？

Question

我有一堆 XML 文件（大约 74k），它们具有这种结构：

<?xml version="1.0" encoding="UTF-8"?><article pmcid="2653499" pmid="19243591" doi="10.1186/1472-6963-9-38">
<title>Systematic review</title>
<fulltext>...</fulltext>
<figures>
<figure iri="1472-6963-9-38-2"><caption>...</caption></figure>
<figure iri="1472-6963-9-38-1"><caption>...</caption></figure>
</figures>
</article>

我想将 pmcid 参数（每个文件唯一）与它们包含在列表中的数字的 iri 参数关联起来，这样我就可以用它们构建一个 numpy 数组甚至是一个易于使用的文件。

例如对于这篇文章，该行应该是：

2653499 1472-6963-9-38-2 1472-6963-9-38-1

我已尝试使用 XSLT，但没有任何结果...我将不胜感激。

Answer 1

这是一个使用标准库中的xml.etree.ElementTree 的选项：

import xml.etree.ElementTree as ET

data = """<?xml version="1.0" encoding="UTF-8"?>
<article pmcid="2653499" pmid="19243591" doi="10.1186/1472-6963-9-38">
    <title>Systematic review</title>
    <fulltext>...</fulltext>
    <figures>
        <figure iri="1472-6963-9-38-2"><caption>...</caption></figure>
        <figure iri="1472-6963-9-38-1"><caption>...</caption></figure>
    </figures>
</article>
"""

article = ET.fromstring(data)

pmcid = article.attrib.get('pmcid')
for figure in article.findall('figures/figure'):
    iri = figure.attrib.get('iri')
    print pmcid, iri

打印：

2653499 1472-6963-9-38-2
2653499 1472-6963-9-38-1

Answer 2

Beautifulsoup 怎么样？

from bs4 import BeautifulSoup

soup = BeautifulSoup(open('file.xml'))

pmcid = soup.find('article')['pmcid']
figure = soup.findAll('figure')

print pmcid,

for i in figure:
    print i['iri'],

完全按照您的示例打印。

2653499 1472-6963-9-38-2 1472-6963-9-38-1

Answer 3

out.xsl：

<!-- http://www.w3.org/TR/xslt#copying -->
<!-- http://www.dpawson.co.uk/xsl/sect2/identity.html#d5917e43 -->
<!-- The Identity Transformation -->
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
    <xsl:output method="text" version="1.0" encoding="UTF-8"/>

    <!-- Whenever you match any node or any attribute -->
    <xsl:template match="@*|node()">
        <!-- Copy the current node -->
        <xsl:copy>
            <!-- Including any attributes it has and any child nodes -->
            <xsl:apply-templates select="@*|node()"/>
        </xsl:copy>
    </xsl:template>

    <xsl:template match="article">
        <xsl:value-of select="@pmcid"/>
        <xsl:apply-templates select="figures/figure"/>
        <xsl:text>
</xsl:text>
    </xsl:template>

    <xsl:template match="figure">
        <xsl:text> </xsl:text><xsl:value-of select="@iri"/>
    </xsl:template>
</xsl:stylesheet>

运行：

$ xsltproc out.xsl in.xml
2653499 1472-6963-9-38-2 1472-6963-9-38-1

Answer 4

你可以试试xmllint。

xmllint --shell myxml <<< `echo 'cat /article/@pmcid|//figures/figure/@*'`
/ >  -------
 pmcid="2653499"
 -------
 iri="1472-6963-9-38-2"
 -------
 iri="1472-6963-9-38-1"
/ >

然后通过管道传送到awk 以获得所需的输出...

xmllint --shell myxml <<< `echo 'cat /article/@pmcid|//figures/figure/@*'` | 
awk -F'[="]' -v ORS=" " 'NF>1{print $3}'
2653499 1472-6963-9-38-2 1472-6963-9-38-1

Answer 5

(A)

好吧，既然你说了任何帮助......这是我的镜头-

根据我的经验，你会更满意的刺激

obj.__dict__

并查看每个 xml 元素如何匹配。这样，您将通过迭代测试（如下）有效地对整个 xml 文件进行拼写检查

我获取了您的示例数据，将其放在 .xml 文件中，并使用 Python IDE (2.7.xxx) 将其加载。以下是我如何编写要使用的代码：

import xml.etree.ElementTree as ET
>>> some_tree = ET.parse("/Users/pro/Desktop/tech/test_scripts/test.xml")
>>> for block_number in range(0, len(some_tree._root.getchildren())):
    print "block_number: " + str(block_number)


block_number: 0
block_number: 1
block_number: 2
>>> some_tree._root.getchildren()
[<Element 'title' at 0x101a59450>, <Element 'fulltext' at 0x101a59550>, <Element 'figures' at 0x101a59410>]
>>> some_tree._root.__dict__
{'text': '\n', 'attrib': {'pmid': '19243591', 'doi': '10.1186/1472-6963-9-38', 'pmcid': '2653499'}, 'tag': 'article', '_children': [<Element 'title' at 0x101a59450>, <Element 'fulltext' at 0x101a59550>, <Element 'figures' at 0x101a59410>]}
>>> some_tree._root.attrib
{'pmid': '19243591', 'doi': '10.1186/1472-6963-9-38', 'pmcid': '2653499'}
>>> some_tree._root.attrib['pmid']
'19243591'
>>> to_store = {}
>>> to_store[some_tree._root.attrib['pmid']] = []
>>> some_tree._root.getchildren()
[<Element 'title' at 0x101a59450>, <Element 'fulltext' at 0x101a59550>, <Element 'figures' at 0x101a59410>]
>>> some_tree._root[2]
<Element 'figures' at 0x101a59410>
>>> some_tree._root[2].__dict__
{'text': '\n', 'attrib': {}, 'tag': 'figures', 'tail': '\n', '_children': [<Element 'figure' at 0x101a595d0>, <Element 'figure' at 0x101a59650>]}
>>> some_tree._root[2].getchildren()
[<Element 'figure' at 0x101a595d0>, <Element 'figure' at 0x101a59650>]
>>> for r in range(0, len(some_tree._root[2].getchildren())):
    print some_tree._root[2].getchildren()[r]


<Element 'figure' at 0x101a595d0>
<Element 'figure' at 0x101a59650>
>>> some_tree._root[2].getchildren()[1].__dict__
{'attrib': {'iri': '1472-6963-9-38-1'}, 'tag': 'figure', 'tail': '\n', '_children': [<Element 'caption' at 0x101a59690>]}
>>> for r in range(0, len(some_tree._root[2].getchildren())):
    to_store[to_store.keys()[0]].append(some_tree._root[2].getchildren()[r].attrib['iri'])


>>> to_store
{'19243591': ['1472-6963-9-38-2', '1472-6963-9-38-1']}
>>> 

请注意，to_store 是任意的，只是为了方便您存储这些 x,y 数据。

B)

我真的很喜欢输出到我自己的 sqlite 平面文件 db.我这样做是为了翻译整本圣经，以便在我发布的 iOS 应用程序运行时使用。以下是 sql 的一些示例代码：

import sqlite3
bible_books = ["genesis", "exodus", "leviticus", "numbers", "deuteronomy",
           "joshua", "judges", "ruth", "1 samuel", "2 samuel", "1 kings",
           "2 kings", "1 chronicles", "2 chronicles", "ezra", "nehemiah",
           "esther", "job", "psalms", "proverbs", "ecclesiastes",
           "song of solomon", "isaiah", "jeremiah", "lamentations",
           "ezekiel", "daniel", "hosea", "joel", "amos", "obadiah",
           "jonah", "micah", "nahum", "habakkuk", "zephaniah", "haggai",
           "zechariah", "malachi", "matthew", "mark", "luke", "john",
           "acts", "romans", "1 corinthians", "2 corinthians",
           "galatians", "ephesians", "philippians", "colossians",
           "1 thessalonians", "2 thessalonians", "1 timothy",
           "2 timothy", "titus", "philemon", "hebrews", "james",
           "1 peter", "2 peter", "1 john", "2 john", "3 john",
           "jude", "revelation"]
chapter_counts = {bible_books[0]:50, bible_books[1]:40, bible_books[2]:27,
          bible_books[3]:36, bible_books[4]:34, bible_books[5]:24,
          bible_books[6]:21, bible_books[7]:4, bible_books[8]:31,
          bible_books[9]:24, bible_books[10]:22, bible_books[11]:25,
          bible_books[12]:29, bible_books[13]:36, bible_books[14]:10,
          bible_books[15]:13, bible_books[16]:10, bible_books[17]:42,
          bible_books[18]:150, bible_books[19]:31, bible_books[20]:12,
          bible_books[21]:8, bible_books[22]:66, bible_books[23]:52,
          bible_books[24]:5, bible_books[25]:48, bible_books[26]:12,
          bible_books[27]:14, bible_books[28]:3, bible_books[29]:9,
          bible_books[30]:1, bible_books[31]:4, bible_books[32]:7,
          bible_books[33]:3, bible_books[34]:3,
          bible_books[35]:3, bible_books[36]:2, bible_books[37]:14,
          bible_books[38]:4, bible_books[39]:28, bible_books[40]:16,
          bible_books[41]:24, bible_books[42]:21, bible_books[43]:28,
          bible_books[44]:16, bible_books[45]:16, bible_books[46]:13,
          bible_books[47]:6, bible_books[48]:6, bible_books[49]:4,
          bible_books[50]:4, bible_books[51]:5, bible_books[52]:3,
          bible_books[53]:6, bible_books[54]:4, bible_books[55]:3,
          bible_books[56]:1, bible_books[57]:13, bible_books[58]:5,
          bible_books[59]:5, bible_books[60]:3, bible_books[61]:5,
          bible_books[62]:1, bible_books[63]:1, bible_books[64]:1,
          bible_books[65]:22}

conn = sqlite3.connect("bible_web.sqlite3")
c = conn.cursor()



for i_book in bible_books:
    book_name = "b_" + i_book.lower().replace(" ", "_")
    for i_chapter in range(1, chapter_counts[i_book]+1):
        c.execute("create table " + book_name + "_" + str(i_chapter) + " (verse real primary key, value text)")

for i_book in bible_books:
    book_name = "b_" + i_book.lower().replace(" ", "_")
    for i_chapter in range(1, chapter_counts[i_book]+1):
        #c.execute("SELECT Count(*) FROM " + book_name + "_" + str(i_chapter))
        #i_rows = int(c.fetchall())
        #for verse_number in range(1, i_rows+1):
        c.execute("update " + book_name + "_" + str(i_chapter) + " set value=trim(value)")

conn.commit()
c.close()
conn.close()

只是一些想法。希望对您有所帮助。