groovy XmlSlurper 无法解析我的 xml 文件

Question

我有一个 xml，但无法使用 xmlslurper 解析该文件。 这里是我的 xml 文件的副本：

<Entrezgene-Set>
<Entrezgene>
<Entrezgene_summary>The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins. [provided by RefSeq]</Entrezgene_summary>
</Entrezgene>
</Entrezgene-Set>

我只需要从 获取文本

这里是我的代码：

  def pubmedEfetch = {

  def base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
  def qs = []
  qs << "db=gene"
  qs << "id=1"
  qs << "retmode=xml"
  def url = new URL(base + qs.join("&"))
  def connection = url.openConnection()

  def result = [:]

  if(connection.responseCode == 200){
    def xml = connection.content.text
    def eFetchResult = new XmlSlurper().parseText(xml)
    result.geneSummary = eFetchResult.Entrezgene-Set.Entrezgene.Entrezgene_summary
  }
  else{
    log.error("PubmedEfetchParserService.PubmedEsearch FAILED")
    log.error(url)
    log.error(connection.responseCode)
    log.error(connection.responseMessage)
  }
  render result
}

以及我的错误消息：

Error 500: groovy.lang.MissingPropertyException: No such property: Entrezgene for class: java.util.Set
Servlet: grails
URI: /geneInfo/grails/genes/pubmedEfetch.dispatch
Exception Message: No such property: Entrezgene for class: java.util.Set 
Caused by: groovy.lang.MissingPropertyException: No such property: Entrezgene for class: java.util.Set 
Class: GenesController 

我不明白我的错在哪里？

我也尝试： result.geneSummary = eFetchResult./Entrezgene-Set/.Entrezgene.Entrezgene_summary

有人有想法吗？ 谢谢

Answer 1

您不需要取消引用顶部标签 (Entersgene-Set>)。以下内容在 groovyconsole 中适用于我：

xml = """<Entrezgene-Set>
<Entrezgene>
   <Entrezgene_summary>The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins. [provided by RefSeq]
   </Entrezgene_summary>
</Entrezgene>
</Entrezgene-Set>
"""


def eFetchResult = new XmlSlurper().parseText(xml)
x = eFetchResult.Entrezgene.Entrezgene_summary
println "x is [${x}]"

顺便说一句，您的错误消息是由于尝试使用带有破折号的属性名称引起的。

Answer 2

谢谢你，
我只是在您的帮助下解决我的问题：

• 通过使用引号，如果我的 xml 元素中有连字符（例如： result.test = eFetchResult.Entrezgene.'Entrezgene_track-info'.'Gene-track'.'Gene-track_geneid' ），
• 通过删除顶部标签引用（如果我保留顶部标签引用，我的地图值为空 - 很高兴知道这一点:-)

这是我的修复：

  def pubmedEfetch = {

  def base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
  def qs = []
  qs << "db=gene"
  qs << "id=1"
  qs << "retmode=xml"
  def url = new URL(base + qs.join("&"))
  def connection = url.openConnection()

  def result = [:]

  if(connection.responseCode == 200){
    def xml = connection.content.text
    def eFetchResult = new XmlSlurper().parseText(xml)
    result.geneSummary = eFetchResult.Entrezgene.Entrezgene_summary
  }
  else{
    log.error("PubmedEfetchParserService.PubmedEsearch FAILED")
    log.error(url)
    log.error(connection.responseCode)
    log.error(connection.responseMessage)
  }
  render result
}