comment on

Hi all,

I am trying to parse an xml file and am encountering errors, I think its to do with using the DTD. Here is part of the xml file:

<?xml version="1.0"?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD eSummaryResult, 29 Octobe
+r 2004//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_04
+1029.dtd">
<eSummaryResult>
<DocSum>
        <Id>7597478</Id>
        <Item Name="Caption" Type="String">NC_002192</Item>
        <Item Name="Title" Type="String">Lactococcus lactis plasmid pW
+V01, complete sequence</Item>
        <Item Name="Extra" Type="String">gi|7597478|ref|NC_002192.1||g
+nl|NCBI_GENOMES|15284[7597478]</Item>
        <Item Name="Gi" Type="Integer">7597478</Item>
        <Item Name="CreateDate" Type="String">1991/04/15</Item>
        <Item Name="UpdateDate" Type="String">2008/04/09</Item>
        <Item Name="Flags" Type="Integer">520</Item>
        <Item Name="TaxId" Type="Integer">1358</Item>
        <Item Name="Length" Type="Integer">2178</Item>
        <Item Name="Status" Type="String">live</Item>
        <Item Name="ReplacedBy" Type="String"></Item>
        <Item Name="Comment" Type="String"><![CDATA[  ]]></Item>
</DocSum>

<DocSum>
        <Id>7597489</Id>
        <Item Name="Caption" Type="String">NC_002193</Item>
        <Item Name="Title" Type="String">Lactococcus lactis cremoris C
+remoris Wg2 plasmid pWVO2, complete sequence</Item>
        <Item Name="Extra" Type="String">gi|7597489|ref|NC_002193.1||g
+nl|NCBI_GENOMES|15285[7597489]</Item>
        <Item Name="Gi" Type="Integer">7597489</Item>
        <Item Name="CreateDate" Type="String">1993/05/10</Item>
        <Item Name="UpdateDate" Type="String">2008/07/17</Item>
        <Item Name="Flags" Type="Integer">776</Item>
        <Item Name="TaxId" Type="Integer">1359</Item>
        <Item Name="Length" Type="Integer">3826</Item>
        <Item Name="Status" Type="String">live</Item>
        <Item Name="ReplacedBy" Type="String"></Item>
        <Item Name="Comment" Type="String"><![CDATA[  ]]></Item>
</DocSum>
[download]

This is my code

#!/usr/bin/perl
use strict;
use warnings;

use XML::LibXML;

  my $public_id = "-//NLM//DTD eSummaryResult, 29 October 2004//EN";
  my $system_id = "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSumma
+ry_041029.dtd";
  my $dtd = XML::LibXML::Dtd->new($public_id, $system_id);

  my $filename='/g/Washu_PopGen/test_gi_docsumms_delVer4.xml';


  my $parser = XML::LibXML->new();
  my $doc    = $parser->parse_file($filename);
  my $outfile ='/g/Washu_PopGen/test_gi_taxid_table.txt';
  $doc ->validate($dtd);

  open(OUTFILE,">",$outfile);

  print OUTFILE join("t", qw(Id TaxId Length Status ReplacedBy))."\n";

foreach my $DocSum ($doc->findnodes('/eSummaryResult/DocSum')) {

        my($Id) = $DocSum->findnodes('./Id');
        print OUTFILE $Id->to_literal, "\t";

        my($TaxId) = $DocSum->findnodes('./TaxId');
        print OUTFILE $TaxId->to_literal, "\t";

        my($Length) = $DocSum->findnodes('./Length');
        print OUTFILE $Length->to_literal, "\t";

        my($Status) = $DocSum->findnodes('./Status');
        print OUTFILE $Status->to_literal, "\t";

        my($ReplacedBy) = $DocSum->findnodes('./ReplacedBy');
        print OUTFILE $ReplacedBy->to_literal, "\n";

  }
[download]

This is part of my Error message

No declaration for element eSummaryResult                             
+                                                                     
+                                                              
No declaration for element DocSum                                     
+                                                                     
+                                                              
No declaration for element Id                                         
+                                                                     
+                                                              
No declaration for element Item                                       
+                                                                     
+                                                              
No declaration for attribute Name of element Item                     
+                                                                     
+                                                              
No declaration for attribute Type of element Item                     
+                                                                     
+                                                              
No declaration for element Item                                       
+                                                                     
+                                                              
No declaration for attribute Name of element Item                     
+                                                                     
+                                                              
No declaration for attribute Type of element Item                     
+                                                                     
+                                                              
No declaration for element Item                                       
+                                                                     
+                                                              
No declaration for attribute Name of element Item                     
+                                                                     
+                                                              
No declaration for attribute Type of element Item
[download]

This is the dtd file

<!--    
This is the Current DTD for Entrez eSummary version 2
$Id: eSummary_041029.dtd 49514 2004-10-29 15:52:04Z parantha $
-->
<!-- =================================================================
+ -->

<!ELEMENT Id                (#PCDATA)>          <!-- \d+ -->

<!ELEMENT Item              (#PCDATA|Item)*>   <!-- .+ -->

<!ATTLIST Item
    Name CDATA #REQUIRED
    Type (Integer|Date|String|Structure|List|Flags|Qualifier|Enumerato
+r|Unknown) #REQUIRED
>

<!ELEMENT ERROR             (#PCDATA)>  <!-- .+ -->

<!ELEMENT DocSum            (Id, Item+)>

<!ELEMENT eSummaryResult    (DocSum|ERROR)+>
[download]

Thanks ! Any help is appreciated

In reply to LibXML and parsing file with DTD by AWallBuilder

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