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groovy xmlslurper不分析我的XML文件

xmlslurper groovy grails xml

2

Fabien Barbier · 技术社区 · 15 年前

我有一个XML,不能用xmlslurper解析这个文件。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 <Entrezgene_summary>

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
}

我的错误信息:

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

我不知道我的错在哪里?

我还尝试:result.genesummary=efetcheresult./enterzgene set/.enterzgene.enterzgene_summary

有人有主意吗? 谢谢

2 回复 | 直到 15 年前

1

5

Jean Barmash 15 年前

您不需要取消对顶部标记的引用(EntersGene set>)。以下内容适用于我在groovyconsole中的工作:

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,您的错误消息是由尝试使用带有破折号的属性名引起的。

2

Fabien Barbier 15 年前

谢谢您, 我只是在你的帮助下解决我的问题:

如果我的xml元素中有连字符(例如:result.test=efetcheresult.enterzgene.'enterzgene'track-info.'gene-track.'gene-track'geneid'),
通过删除,顶部标记引用(如果保留顶部标记引用,则我的映射值为空-很好地知道:—)

这里是我的修复:

  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
}