Search code examples
rubyxmlnokogiriruby-on-rails-2

Collecting Attributes in XML using Nokogiri

I have this 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>

I am able to retrieve all the element tags mainly EXPERIMENT, ERROR, INFO, ACTION, MESSAGE.

What I would like to retrieve is the attributes from elements like EXPERIMENT and RECEIPT

I am using Nokogiri for my parsing.

My code is like this:

@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")

That was my controller. My View is something just for display:

<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 %>

and the application renders something like this:

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

Please could someone suggest the retrieving method/option.

Solution

  • It's not clear to me what you are trying to do, or what your problem is. Below are a variety of answers that might help.

    For any element you can use Nokogiri::XML::Node#attributes to get a hash mapping the name of the node to a Nokogiri::XML::Attr (which has a .value you can read):

    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>

    Instead of attributes (a Hash) you can also use .attribute_nodes, which gives you a straight array of Attrs (with a .name and .value each).

    Alternatively, while iterating through your experiment elements you could use…

    <%= expt['alias'] %>

    …to extract the value of a known attribute (returning a string such as "ENT 23").

    If you're trying to extract all the attributes on their own, you could also use…

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

    …if you wanted to get an array of just those attributes anywhere in the document (which have a .name and .value).

    If you only want all the alias attributes on a particular element (e.g. EXPERIMENT) then you can use…

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