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Full Discussion: How to extract data from XML file using shell scripting?
Top Forums Shell Programming and Scripting How to extract data from XML file using shell scripting? Post 302843129 by arun_kohan on Monday 12th of August 2013 06:55:47 AM
Old 08-12-2013
How to extract data from XML file using shell scripting?
Hi ,
I have input file as XML. following are input data
#complex.xml


Code:
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.
Code:
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 ...

Thanks in advance..
Last edited by joeyg; 08-12-2013 at 09:08 AM.. Reason: CodeTags for all data and commands
 

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LEARN ABOUT SUSE

xmlstarlet

XMLSTARLET(1)							 xmlstarlet Manual						     XMLSTARLET(1)

NAME

       xmlstarlet - command line XML/XSLT toolkit

SYNOPSIS

       xmlstarlet [<options>] [<command>] [<cmd-options>]

INTRODUCTION

       XMLStarlet is a set of command line utilities (tools) which can be used to transform, query, validate, and edit XML documents and files us-
       ing simple set of shell commands in similar way it is done for plain text files using UNIX grep, sed, awk, diff, patch, join, etc commands.
       This  set of command line utilities can be used by those who deal with many XML documents on UNIX shell command prompt as well as for auto-
       mated XML processing with shell scripts.

OPTIONS

       --version
	      Display the version of xmlstarlet.

       --help Display help.

COMMANDS

       Type: xml <command> --help <ENTER> for command help

       Available commands include:

       ed (or edit)
	      Edit/update XML document(s).

       sel (or select)
	      Select data or query XML document(s) (XPATH, etc).

       tr (or transform)
	      Transform XML documents(s) using XSLT.

       val (or validate)
	      Validate XML document(s) (well-formed/DTD/XSD/RelaxNG).

       fo (or format)
	      Format XML document(s).

       el (or elements)
	      Display element structure of XML document.

       c14n (or canonic)
	      XML canonicalization.

       ls (or list)
	      List directory as XML.

       esc (or escape)
	      Escape special XML characters.

       unesc (or unescape)
	      Unescape special XML characters.

       pyx (or xmln)
	      Convert XML into PYX format (based on ESIS - ISO 8879).

       p2x (or depyx)
	      Convert PYX into XML.

REFERENCES

       XMLStarlet is a command line  toolkit  to  query/edit/check/transform  XML  documents  (for  more  information  see  http://xmlstar.source-
       forge.net/).

AUTHOR

       Mikhail Grushinskiy.

																     XMLSTARLET(1)
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