NotXMLError：无法解析 XML 数据

Question

我正在尝试使用 Biopython 中的 Entrez 模块从 PubMed Central 检索全文文章。这是我做同样事情的代码。

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() 有效，这意味着数据已正确获取。但是，我无法将获取的数据转换为 python 对象。它给了我以下错误：

Entrez.read(handle)

有人可以告诉我该怎么办吗？根据 biopython 文档，这似乎是正确的语法。

Answer 1

uri

http://www.niso.org/schemas/ali/1.0/ 的 DTD。 GitHub 版本具有更正的 Parser，但现在无法从 NotXMLError: Failed to parse the XML data (syntax error: line 1036, column 69). Please make sure that the input data are in XML format. 获得。 比较：

当前1.79

pip

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"
            else:
                raise ValueError("Unknown prefix '%s' with uri '%s'" % (prefix, uri))
            self.namespace_level[prefix] += 1
            self.namespace_prefix[uri] = prefix

因此您可以交换或编辑 

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全文，您可以尝试通过

---

    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

下载 pdf 并继续通过

metapub

提取文本。textract

Answer 2