lxml:将命名空间添加到输入文件

Question

我正在解析一个由外部program生成的xml文件。然后，我想使用我自己的命名空间向该文件添加自定义注释。我的输入如下所示：

<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
  <model metaid="untitled" id="untitled">
    <annotation>...</annotation>
    <listOfUnitDefinitions>...</listOfUnitDefinitions>
    <listOfCompartments>...</listOfCompartments>
    <listOfSpecies>
      <species metaid="s1" id="s1" name="GenA" compartment="default" initialAmount="0">
        <annotation>
          <celldesigner:extension>...</celldesigner:extension>
        </annotation>
      </species>
      <species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
        <annotation>
           <celldesigner:extension>...</celldesigner:extension>
        </annotation>
      </species>
    </listOfSpecies>
    <listOfReactions>...</listOfReactions>
  </model>
</sbml>

问题是，lxml只在使用名称空间时声明它们，这意味着声明会重复多次，如下所示(简化)：

<sbml xmlns="namespace" xmlns:celldesigner="morenamespace" level="2" version="4">
  <listOfSpecies>
    <species>
      <kjw:test xmlns:kjw="http://this.is.some/custom_namespace"/>
      <celldesigner:data>Some important data which must be kept</celldesigner:data>
    </species>
    <species>
      <kjw:test xmlns:kjw="http://this.is.some/custom_namespace"/>
    </species>
    ....
  </listOfSpecies>
</sbml>

是否可以强制lxml在父元素(如sbml或listOfSpecies )中只编写一次此声明？或者，有没有好的理由不这么做？我想要的结果是：

<sbml xmlns="namespace" xmlns:celldesigner="morenamespace" level="2" version="4"  xmlns:kjw="http://this.is.some/custom_namespace">
  <listOfSpecies>
    <species>
      <kjw:test/>
      <celldesigner:data>Some important data which must be kept</celldesigner:data>
    </species>
    <species>
      <kjw:test/>
    </species>
    ....
  </listOfSpecies>
</sbml>

重要的问题是，从文件中读取的现有数据必须保留，因此我不能只创建一个新的根元素(我认为？)。

编辑:代码附在下面。

def annotateSbml(sbml_input):
  from lxml import etree

  checkSbml(sbml_input) # Makes sure the input is valid sbml/xml.

  ns = "http://this.is.some/custom_namespace"
  etree.register_namespace('kjw', ns)

  sbml_doc = etree.ElementTree()
  root = sbml_doc.parse(sbml_input, etree.XMLParser(remove_blank_text=True))
  nsmap = root.nsmap
  nsmap['sbml'] = nsmap[None] # Makes code more readable, but seems ugly. Any alternatives to this?
  nsmap['kjw'] = ns
  ns = '{' + ns + '}'
  sbmlns = '{' + nsmap['sbml'] + '}'

  for species in root.findall('sbml:model/sbml:listOfSpecies/sbml:species', nsmap):
    species.append(etree.Element(ns + 'test'))

  sbml_doc.write("test.sbml.xml", pretty_print=True, xml_declaration=True)

  return

Answer 1

在lxml中不能修改节点的名称空间映射。请参阅将此功能作为愿望列表项的this open ticket。

它起源于lxml邮件列表中的this thread，其中给出了一个workaround replacing the root node作为替代。不过，替换根节点有一些问题:请参阅上面的票证。

为了完整起见，我将建议的根目录替换解决方法代码放在这里：

>>> DOC = """<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
...   <model metaid="untitled" id="untitled">
...     <annotation>...</annotation>
...     <listOfUnitDefinitions>...</listOfUnitDefinitions>
...     <listOfCompartments>...</listOfCompartments>
...     <listOfSpecies>
...       <species metaid="s1" id="s1" name="GenA" compartment="default" initialAmount="0">
...         <annotation>
...           <celldesigner:extension>...</celldesigner:extension>
...         </annotation>
...       </species>
...       <species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
...         <annotation>
...            <celldesigner:extension>...</celldesigner:extension>
...         </annotation>
...       </species>
...     </listOfSpecies>
...     <listOfReactions>...</listOfReactions>
...   </model>
... </sbml>"""
>>> 
>>> from lxml import etree
>>> from StringIO import StringIO
>>> NS = "http://this.is.some/custom_namespace"
>>> tree = etree.ElementTree(element=None, file=StringIO(DOC))
>>> root = tree.getroot()
>>> nsmap = root.nsmap
>>> nsmap['kjw'] = NS
>>> new_root = etree.Element(root.tag, nsmap=nsmap)
>>> new_root[:] = root[:]
>>> new_root.append(etree.Element('{%s}%s' % (NS, 'test')))
>>> new_root.append(etree.Element('{%s}%s' % (NS, 'test')))

>>> print etree.tostring(new_root, pretty_print=True)
<sbml xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" xmlns:kjw="http://this.is.some/custom_namespace" xmlns="http://www.sbml.org/sbml/level2/version4"><model metaid="untitled" id="untitled">
    <annotation>...</annotation>
    <listOfUnitDefinitions>...</listOfUnitDefinitions>
    <listOfCompartments>...</listOfCompartments>
    <listOfSpecies>
      <species metaid="s1" id="s1" name="GenA" compartment="default" initialAmount="0">
        <annotation>
          <celldesigner:extension>...</celldesigner:extension>
        </annotation>
      </species>
      <species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
        <annotation>
           <celldesigner:extension>...</celldesigner:extension>
        </annotation>
      </species>
    </listOfSpecies>
    <listOfReactions>...</listOfReactions>
  </model>
<kjw:test/><kjw:test/></sbml>

Answer 2

我知道这是一个老问题，但它仍然有效，从lxml 3.5.0开始，可能有更好的解决方案：

cleanup_namespaces()接受一个新参数top_nsmap，该参数将所提供的前缀名称空间映射的定义移动到树的顶部。

因此，现在只需调用以下命令即可将名称空间映射上移：

nsmap = {'kjw': 'http://this.is.some/custom_namespace'}
etree.cleanup_namespaces(root, top_nsmap=nsmap)

Answer 3

如果临时将命名空间属性添加到根节点，则可以做到这一点。

ns = '{http://this.is.some/custom_namespace}'

# add 'kjw:foobar' attribute to root node
root.set(ns+'foobar', 'foobar')

# add kjw namespace elements (or attributes) elsewhere
... get child element species ...
species.append(etree.Element(ns + 'test'))

# remove temporary namespaced attribute from root node
del root.attrib[ns+'foobar']