使用 Nokogiri 收集 XML 中的属性

Question

我有这个 XML：

<RECEIPT receiptDate="2012-02-10T12:46:26.661Z" submissionFile="E.coli_ENT_WS.submission.xml" success="false">

  <EXPERIMENT alias="ENT 23" status="PUBLIC"/>
  <EXPERIMENT alias="WS 23" status="PUBLIC"/>
  <RUN alias="ENT 23" status="PUBLIC"/>
  <RUN alias="WS 23" status="PUBLIC"/><
  SAMPLE alias="ENT 23" status="PUBLIC"/>
  <SAMPLE alias="WS 23" status="PUBLIC"/>
  <STUDY alias="ENT 23" status="PUBLIC"/>
  <STUDY alias="WS 23" status="PUBLIC"/>
  <SUBMISSION alias="E.coli_ENT_WS"/>
  <MESSAGES>
    <ERROR> In run(ENT 23), the FC018_s_6_sequence_L70.txt.md5 not found </ERROR>
    <ERROR> In run(ENT 23) found the file format(Illumina_native_fastq), but requires SPOT_DESCRIPTOR information in the experiment(ENT 23)</ERROR>
    <ERROR>The Illumina_native_fastq file format required gzip compression for submission.</ERROR>
    <ERROR> FILE attribute quality_scoring_system is required</ERROR>
    <ERROR>Same file FC018_s_6_sequence_L70.txt found in Run(WS 23) has been used with other Run</ERROR>
    <ERROR> In run(WS 23), the FC018_s_6_sequence_L70.txt.md5 not found </ERROR>
    <ERROR> In run(WS 23) found the file format(Illumina_native_fastq), but requires SPOT_DESCRIPTOR information in the experiment(WS 23)</ERROR>
    <ERROR>The Illumina_native_fastq file format required gzip compression for submission.</ERROR>
    <ERROR> FILE attribute quality_scoring_system is required</ERROR>
    <INFO> VALIDATE action for the following XML: E.coli_ENT_WS.study.xml E.coli_ENT_WS.sample.xml E.coli_ENT_WS.experiment.xml E.coli_ENT_WS.run.xml      </INFO>
    <INFO>Inform_on_error is not filled in; auto populated from Submission account. </INFO>
    <INFO>Number of files in drop box = 2 &amp; Number of files in Submission = 1</INFO>
    <INFO>Deprecated element ignored: CENTER_NAME</INFO>
    <INFO>Deprecated element PROJECT_ID converted to RELATED_STUDY</INFO>
    <INFO>Deprecated element ignored: CENTER_NAME</INFO>
    <INFO>Deprecated element PROJECT_ID converted to RELATED_STUDY</INFO>
    <INFO> SPOT_DESCRIPTOR is missing</INFO><INFO> SPOT_DESCRIPTOR is missing</INFO>
    <INFO>Experiment (ENT 23) SPOTDESCRIPTOR is optional is null</INFO>
    <INFO>Experiment (WS 23) SPOTDESCRIPTOR is optional is null</INFO>
    <INFO> In run(ENT 23) file name (FC018_s_6_sequence_L70.txt) mentioned is not found among the submitted files</INFO>
    <INFO> In run(WS 23) file name (FC018_s_6_sequence_L70.txt) mentioned is not found among the submitted files</INFO>
  </MESSAGES>
  <ACTIONS>VALIDATE</ACTIONS>
  <ACTIONS>VALIDATE</ACTIONS>
  <ACTIONS>VALIDATE</ACTIONS>
  <ACTIONS>VALIDATE</ACTIONS>
  <ACTIONS>HOLD</ACTIONS>
</RECEIPT>

我能够检索所有元素标签，主要是EXPERIMENT、ERROR、INFO、ACTION、MESSAGE。

我想检索的是来自 EXPERIMENT 和 RECEIPT 等元素的属性

我正在使用 Nokogiri 进行解析。

我的代码是这样的：

@req_test = %x[curl -F "SUBMISSION=@xml/#{@experiment.alias}.submission.xml" -F "STUDY=@xml/#{@experiment.alias}.study.xml" -F "SAMPLE=@xml/#{@experiment.alias}.sample.xml" -F "RUN=@xml/#{@experiment.alias}.run.xml" -F "EXPERIMENT=@xml/#{@experiment.alias}.experiment.xml" https://www-test.ebi.ac.uk/ena/submit/drop-box/submit/]
    @doc = Nokogiri::XML(@req_test) 

    # collecting all the errors
    @expt = @doc.xpath("//ERROR")

    # Collecting all the INFO
    @info = @doc.xpath("//INFO")

那是我的控制器。我的观点只是为了展示：

<h3>This is the ERRORS Collected</h3>
<% for expt in @expt %>
<ul>
  <li><%= expt %><br \></li>
</ul>
<% end %>

<br \ >

<h3>This is the INFO Collected</h3>

<% for info in @info %>
<ul>
  <li><%= info %><br \></li>
</ul>
<% end %>

应用程序呈现如下内容：

This is the ERRORS Collected

    In run(ENT 23), the FC018_s_6_sequence_L70.txt.md5 not found

    In run(ENT 23) found the file format(Illumina_native_fastq), but requires SPOT_DESCRIPTOR information in the experiment(ENT 23)

    The Illumina_native_fastq file format required gzip compression for submission.

    FILE attribute quality_scoring_system is required

    Same file FC018_s_6_sequence_L70.txt found in Run(WS 23) has been used with other Run

    In run(WS 23), the FC018_s_6_sequence_L70.txt.md5 not found

    In run(WS 23) found the file format(Illumina_native_fastq), but requires SPOT_DESCRIPTOR information in the experiment(WS 23)

    The Illumina_native_fastq file format required gzip compression for submission.

    FILE attribute quality_scoring_system is required


This is the INFO Collected

    VALIDATE action for the following XML: E.coli_ENT_WS.study.xml E.coli_ENT_WS.sample.xml E.coli_ENT_WS.experiment.xml E.coli_ENT_WS.run.xml

    Inform_on_error is not filled in; auto populated from Submission account.

    Number of files in drop box = 2 & Number of files in Submission = 1

    Deprecated element ignored: CENTER_NAME

    Deprecated element PROJECT_ID converted to RELATED_STUDY

    Deprecated element ignored: CENTER_NAME

    Deprecated element PROJECT_ID converted to RELATED_STUDY

    SPOT_DESCRIPTOR is missing

    SPOT_DESCRIPTOR is missing

    Experiment (ENT 23) SPOTDESCRIPTOR is optional is null

    Experiment (WS 23) SPOTDESCRIPTOR is optional is null

    In run(ENT 23) file name (FC018_s_6_sequence_L70.txt) mentioned is not found among the submitted files

    In run(WS 23) file name (FC018_s_6_sequence_L70.txt) mentioned is not found among the submitted files

请有人建议检索方法/选项。

Answer 1

我不清楚你想做什么，或者你的问题是什么。以下是可能有帮助的各种答案。

对于任何元素，您都可以使用Nokogiri::XML::Node#attributes 获取将节点名称映射到Nokogiri::XML::Attr 的哈希值（其中有一个.value，您可以阅读）：

require 'nokogiri'
require 'erb'

template = <<ENDERB
<% unless @expts.empty? %>
<h3>Experiments</h3>
<ul><% for expt in @expts %>
  <li><%= expt %><ul>
    <% expt.attributes.each do |name,attr| %>
      <li><%=name%> = <%=attr.value%></li>
    <% end %>
  </ul></li>
<% end %></ul>
<% end %>
ENDERB

doc = Nokogiri.XML(DATA)
@expts = doc.xpath("//EXPERIMENT")   
puts ERB.new(template).result(binding).gsub(/^[ \t]*\n/,'')
#=> <h3>Experiments</h3>
#=> <ul>
#=>   <li><EXPERIMENT alias="ENT 23" status="PUBLIC"/><ul>
#=>       <li>alias = ENT 23</li>
#=>       <li>status = PUBLIC</li>
#=>   </ul></li>
#=>   <li><EXPERIMENT alias="WS 23" status="PUBLIC"/><ul>
#=>       <li>alias = WS 23</li>
#=>       <li>status = PUBLIC</li>
#=>   </ul></li>
#=> </ul>

除了attributes（哈希），您还可以使用.attribute_nodes，它为您提供Attrs 的直接数组（每个.name 和.value）。

或者，在迭代您可以使用的实验元素时……

<%= expt['alias'] %>

…提取已知属性的值（返回字符串，例如"ENT 23"）。

如果你想自己提取所有属性，你也可以使用…

@aliases = @doc.xpath('//@alias')

...如果您想在文档中的任何位置（具有.name 和.value）获取这些属性的数组。

如果您只想要特定元素上的所有alias 属性（例如EXPERIMENT），那么您可以使用...

@expt_aliases = @doc.xpath('//EXPERIMENT/@alias')