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Full Discussion: Extract data from XML file
Top Forums Shell Programming and Scripting Extract data from XML file Post 302773507 by mohan sharma on Thursday 28th of February 2013 05:44:26 AM
Old 02-28-2013
Extract data from XML file
Hi ,
I have input file as XML. following are input data
#complex.xml
Code:
<?xml version="1.0" encoding="UTF-8"?>
<TEST_doc xmlns="http://www.w3.org/2001/XMLSchema-instance">
  <ENTRY uid="123456">
    <protein>
      <name>PROT001</name>
      <organism>Human</organism>
      <class>cytoplasmic</class>
    </protein>
    <xrefs>
      <xref>
          <database>Ensembl</database>
          <accn>ENSG00000105829</accn>
      </xref>
      <xref>
          <database>UNIPROT</database>
          <accn>Q12345</accn>
      </xref>
    </xrefs>
  </ENTRY>
  <ENTRY uid="45678">
    <protein>
      <name>PROT002</name>
      <organism>Human</organism>
      <class>nuclear</class>
    </protein>
    <xrefs>
      <xref>
          <database>Ensembl</database>
          <accn>ENSG00000105333</accn>
      </xref>
      <xref>
          <database>UNIPROT</database>
          <accn>Q14789</accn>
      </xref>
    </xrefs>
  </ENTRY>
</TEST_doc>

i want to extract data from this file and i tried below query.
cat complex.xml | xml sel -t -m //xref -v "concat(../../protein/name,' ',../../protein/class,' ',./database,' ',./accn)" -n

but it is not giving any output...but this query is working when instead of xmlns i am writing xmlns:xsi="...."
but my input file is having only xmlns="..."

please help me ...
Last edited by fpmurphy; 02-28-2013 at 09:53 AM..
 

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LEARN ABOUT DEBIAN

hwloc-assembler

HWLOC-ASSEMBLER(1)						       hwloc							HWLOC-ASSEMBLER(1)

NAME

       hwloc-assembler - Assemble multiple XML topologies

SYNOPSIS

       hwloc-assembler [options] output.xml [--name <name1>] input1.xml [--name <name2>] input2.xml ...

OPTIONS

       -n --name <name>
	      Set <name> in the AssemblerName info attribute of the next input topology root to ease identification within the final global topol-
	      ogy.

       -f --force
	      Ignore errors while reading input files.

       -v --verbose
	      Verbose messages.

DESCRIPTION

       hwloc-assembler combines the input XML topologies and exports the resulting global topologies to a new XML file.  All inputs are  inserting
       as children of the global root object.  Each input topology root is annotated with info attributes before insertion.  AssemblerIndex is set
       to the index within the list of inputs.	AssemblerName is set to the name given with --name if any.  hwloc-assembler-remote offers a  fron-
       tend for assembling remote nodes topologies without having to manually gather and transfer each of them.

EXAMPLES

       To assemble two nodes topologies:

	   $ hwloc-assembler output.xml --name host1 host1.xml --name host2 host2.xml

RETURN VALUE

       Upon successful execution, hwloc-assembler returns 0.

       hwloc-assembler will return nonzero if any kind of error occurs, such as (but not limited to) failure to parse the command line.

SEE ALSO

       hwloc(7), lstopo(1), hwloc-assembler-remote(1)

1.4.1								   Feb 27, 2012 						HWLOC-ASSEMBLER(1)
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