NOTXMLERROR：无法解析XML数据

Question

我正在尝试使用来自Biopython的Entrez模块来从PubMed Central检出全文文章。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)

hander.read（）工作，这意味着数据正在正确获取。但是，我无法执行entrez.read（handle）将获取的数据转换为Python对象。它给我以下错误：

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

有人可以告诉我该怎么办？根据《生物闻》文档，这似乎是正确的语法。

Answer 1

原因是最后一个可用的生物繁殖版本（1.79）未用 uri http://www.niso.org/schemas/ali/1.0/ 。 GitHub版本具有更正的 Parser ，但现在无法从pip中获得。
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

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的全文，则可以尝试通过metapub＆amp;尝试下载PDF。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",
    ))

Answer 2

我更新生物繁殖后再次提出了此错误。我使用retrieveng XML通过Esummary的代码表现良好，但最近我没有使用相同的代码重现结果。我进入了Parser.py代码，现在它具有ALI符号。但是生物繁殖失败在解析XML形式的输出中。