python - lxml:来自 URL 的一些 XML 给出了这个 lxml.etree.XMLSyntaxError

Question

我有一个脚本，可以从 URL 列表的 XML 文件中提取一些术语。所有 URL 都可以访问 XML 数据。

它在第一次正确打开、解析和提取时工作正常，但随后在过程中被某些 XML 文件中断并出现此错误:

File "<stdin>", line 18, in <module>
  File "lxml.etree.pyx", line 2953, in lxml.etree.parse (src/lxml/lxml.etree.c:56204)
  File "parser.pxi", line 1555, in lxml.etree._parseDocument (src/lxml/lxml.etree.c:82511)
  File "parser.pxi", line 1585, in lxml.etree._parseFilelikeDocument (src/lxml/lxml.etree.c:82832)
  File "parser.pxi", line 1468, in lxml.etree._parseDocFromFilelike (src/lxml/lxml.etree.c:81688)
  File "parser.pxi", line 1024, in lxml.etree._BaseParser._parseDocFromFilelike (src/lxml/lxml.etree.c:78735)
  File "parser.pxi", line 569, in lxml.etree._ParserContext._handleParseResultDoc (src/lxml/lxml.etree.c:74472)
  File "parser.pxi", line 650, in lxml.etree._handleParseResult (src/lxml/lxml.etree.c:75363)
  File "parser.pxi", line 590, in lxml.etree._raiseParseError (src/lxml/lxml.etree.c:74696)
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1

根据我的搜索，可能是因为某些 XML 文件有空格，但我不确定这是否是问题所在。我不知道是哪个文件出错了。有办法解决这个错误吗？

这是我的脚本:

URLlist = ["http://www.uniprot.org/uniprot/"+x+".xml" for x in IDlist]
for id, item in zip(IDlist, URLlist):
    goterm_location = []
    goterm_function = []
    goterm_process = []
    location_list[id] = []
    function_list[id] = []
    biological_list[id] = []
    try:
        textfile = urllib2.urlopen(item);
    except urllib2.HTTPError:
        print("URL", item, "could not be read.")
        continue
    #Try to solve empty line error#
    tree = etree.parse(textfile);
    #root = tree.getroot()
    for node in tree.iter('{http://uniprot.org/uniprot}dbReference'):
        if node.attrib.get('type') == 'GO':
            for child in node:
                value = child.attrib.get('value');
                if value.startswith('C:'):
                    goterm_C = node.attrib.get('id')
                    if goterm_C:
                        location_list[id].append(goterm_C);
                if value.startswith('F:'):
                    goterm_F = node.attrib.get('id')
                    if goterm_F:
                        function_list[id].append(goterm_F);
                if value.startswith('P:'):
                    goterm_P = node.attrib.get('id')
                    if goterm_P:
                        biological_list[id].append(goterm_P);

我试过:

tree = etree.iterparse(textfile, events = ("start","end"));
OR
parser = etree.XMLParser(remove_blank_text=True)
tree = etree.parse(textfile, parser)

没有成功。任何帮助将不胜感激

Answer 1

I can't tell which files give the error

通过在解析之前打印文件名/U​​RL 进行调试。然后您将看到导致错误的文件。

另外，阅读错误信息:

lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1

这表明下载的 XML 文件是空的。确定导致问题的 URL 后，请尝试下载文件并检查其内容。我怀疑它可能是空的。

您可以在解析时使用 try/except block 来忽略有问题的文件(空文件或其他语法无效的文件):

try:
    tree = etree.parse(textfile)
except lxml.etree.XMLSyntaxError:
    print 'Skipping invalid XML from URL {}'.format(item)
    continue    # go on to the next URL

或者您可以通过检查“Content-length” header 来检查空文件，或者甚至通过读取 urlopen() 返回的资源来检查空文件，但我认为上面的方法更好，因为它还将捕获其他潜在错误。