NotXMLError: Failed to parse the XML data

Question

我试图使用来自bioppython的Entrez模块从PubMed Central检索全文文章。这是我做同样的代码。

import urllib3
import json
import requests
from Bio import Entrez
from Bio.Entrez import efetch, Parser
print(Parser.__file__)
pmcid = 'PMC2837563'
def print_text(pmcid):
handle = efetch(db='pmc', id=pmcid, retmode='xml', rettype=None)
#print(handle.read())
record = Entrez.read(handle)
print(record)
print_text(pmcid)

handle.read()工作，这意味着数据正在被正确获取。但是，我不能做Entrez.read(handle)将获取的数据转换成python对象。它给了我下面的错误:

NotXMLError: Failed to parse the XML data (syntax error: line 1036, column 69). Please make sure that the input data are in XML format.

谁能告诉我该怎么做?根据bioppython文档，这似乎是正确的语法。

Answer 1

原因是最后可用的bioppython版本(1.79)不识别带有urihttp://www.niso.org/schemas/ali/1.0/的DTD。GitHub版本有更正的解析器，但现在pip中不可用。比较:

当前1.79

def startNamespaceDeclHandler(self, prefix, uri):
"""Handle start of an XML namespace declaration."""
if prefix == "xsi":
# This is an xml schema
self.schema_namespace = uri
self.parser.StartElementHandler = self.schemaHandler
else:
# Note that the DTD for MathML specifies a default attribute
# that declares the namespace for each MathML element. This means
# that MathML element in the XML has an invisible MathML namespace
# declaration that triggers a call to startNamespaceDeclHandler
# and endNamespaceDeclHandler. Therefore we need to count how often
# startNamespaceDeclHandler and endNamespaceDeclHandler were called
# to find out their first and last invocation for each namespace.
if prefix == "mml":
assert uri == "http://www.w3.org/1998/Math/MathML"
elif prefix == "xlink":
assert uri == "http://www.w3.org/1999/xlink"
else:
raise ValueError("Unknown prefix '%s' with uri '%s'" % (prefix, uri))
self.namespace_level[prefix] += 1
self.namespace_prefix[uri] = prefix

GitHub

def startNamespaceDeclHandler(self, prefix, uri):
"""Handle start of an XML namespace declaration."""
if prefix == "xsi":
# This is an xml schema
self.schema_namespace = uri
self.parser.StartElementHandler = self.schemaHandler
else:
# Note that the DTD for MathML specifies a default attribute
# that declares the namespace for each MathML element. This means
# that MathML element in the XML has an invisible MathML namespace
# declaration that triggers a call to startNamespaceDeclHandler
# and endNamespaceDeclHandler. Therefore we need to count how often
# startNamespaceDeclHandler and endNamespaceDeclHandler were called
# to find out their first and last invocation for each namespace.
if prefix == "mml":
assert uri == "http://www.w3.org/1998/Math/MathML"
elif prefix == "xlink":
assert uri == "http://www.w3.org/1999/xlink"
elif prefix == "ali":
assert uri == "http://www.niso.org/schemas/ali/1.0/"
else:
raise ValueError(f"Unknown prefix '{prefix}' with uri '{uri}'")
self.namespace_level[prefix] += 1
self.namespace_prefix[uri] = prefix

你可以交换或编辑Parser.py文件，或使用第三方库将句柄转换为内置python对象。

---

如果您只想下载文章的全文，您可以尝试通过metapub&继续通过textract提取文本

import metapub
from urllib.request import urlretrieve
import textract
pmcid = 'PMC2837563'
fetch = metapub.PubMedFetcher()
article_metadata = fetch.article_by_pmcid(pmcid)
#Get just an abstract
abstract = article_metadata.abstract
#Download full article text
pmid = article_metadata.pmid
url = metapub.FindIt(pmid).url
urlretrieve(url, any_path)
with open(another_path, "w") as textfile:
textfile.write(textract.process(
any_path,
extension='pdf',
method='pdftotext',
encoding="utf_8",
))