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 & 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
。
我想要检索的是EXPERIMENT
和RECEIPT
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")
那是我的控制者。我的观点仅供展示:
<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 %>
并且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。
答案 0 :(得分:1)
我不清楚你要做什么,或者你的问题是什么。以下是可能有所帮助的各种答案。
对于任何元素,您可以使用Nokogiri::XML::Node#attributes
来获取哈希映射,将节点名称映射到Nokogiri::XML::Attr
(您可以阅读.value
):
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>
您可以使用.attribute_nodes
代替attributes
(哈希),它会为您提供一系列Attr
s(.name
和.value
每个)。
或者,在迭代实验元素时,您可以使用...
<%= expt['alias'] %>
...提取已知属性的值(返回"ENT 23"
等字符串。)
如果您尝试自行提取所有属性,也可以使用...
@aliases = @doc.xpath('//@alias')
...如果您想在文档中的任何位置(包含.name
和.value
)获取这些属性的数组。
如果您只想要特定元素的所有alias
属性(例如EXPERIMENT
),那么您可以使用...
@expt_aliases = @doc.xpath('//EXPERIMENT/@alias')