lxml:将命名空间添加到输入文件

时间:2012-07-05 14:30:47

标签: python xml namespaces lxml

我正在解析由外部program生成的xml文件。然后,我想使用自己的命名空间向此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只在使用时声明名称空间,这意味着声明会重复多次,如此(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仅在父元素中编写此声明一次,例如sbmllistOfSpecies?或者有充分的理由不这样做吗?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>

重要的问题是必须保留从文件中读取的现有数据,所以我不能只创建一个新的根元素(我想?)。

编辑:下面附带的代码。

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

6 个答案:

答案 0 :(得分:9)

在lxml中无法修改节点的命名空间映射。请参阅具有此功能的this open ticket作为愿望清单项目。

它起源于lxml邮件列表中的this thread,其中workaround replacing the root node作为替代。但是更换根节点存在一些问题:请参阅上面的票证。

为了完整起见,我会在此处提供建议的根替换解决方法代码:

>>> 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>

答案 1 :(得分:3)

除了直接处理原始XML之外,您还可以查看LibSBML,这是一个用于操作SBML文档的库,其中包含python等语言绑定。你可以这样使用它:

>>> from libsbml import *
>>> doc = readSBML('Dropbox/SBML Models/BorisEJB.xml')
>>> species = doc.getModel().getSpecies('MAPK')
>>> species.appendAnnotation('<kjw:test xmlns:kjw="http://this.is.some/custom_namespace"/>')
0
>>> species.toSBML()
'<species id="MAPK" compartment="compartment" initialConcentration="280" boundaryCondition="false">\n  <annotation>\n
 <kjw:test xmlns:kjw="http://this.is.some/custom_namespace"/>\n  </annotation>\n</species>'
>>>

答案 2 :(得分: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来解决这个问题:

  

cleanup_namespaces()接受一个新参数top_nsmap,它将提供的prefix-namespace映射的定义移动到树的顶部。

现在可以通过简单的调用来移动命名空间映射:

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

答案 3 :(得分:1)

如果您暂时将命名空间属性添加到根节点,那就可以了。

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']

答案 4 :(得分:0)

您可以替换根元素以将“kjw”添加到其nsmap。然后xmlns声明只在根元素中。

答案 5 :(得分:0)

我编写了此函数,以便在根元素中添加名称空间:

def addns(tree, alias, uri):                
    root = tree.getroot()
    nsmap = root.nsmap
    nsmap[alias] = uri
    new_root = etree.Element(root.tag, attrib=root.attrib, nsmap=nsmap)
    new_root[:] = root[:]
    return new_root.getroottree()

应用此功能后,您将获得一棵新树,但是您可以通过访问该树的单个对象更改树实例 ...,因为您具有强大的OO设计!