in reply to parsing multiple xml files with xml::twig

Did you "use strict" and "use warnings"?

You are defining the variable $twig in the foreach loop, but trying to access it in the "parse_twig" sub (i.e. out of scope!).

You will save (thanx Jenda ;) a lot of time if you use ALWAYS the "use strict" and "use warnings" pragmas in your scripts.

citromatik

  • Comment on Re: parsing multiple xml files with xml::twig

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Re^2: parsing multiple xml files with xml::twig
by diomedea (Sexton) on Jun 08, 2007 at 09:54 UTC
    thanks, yes i did have use strict and warnings enabled, Im not sure its a scoping issue as the $twig is a global and it does run without giving errors, just not the results I expected!
    if I put all the sub code into the foreach loop I still get the same problem, namely that the last file is the only one which is apparently parsed: I missed some bits of code out before as I didnt think they were relevant and was trying to avoid inflating the post with unimportant details.. heres the fuller version: 
    #! /usr/bin/perl -wT


use strict;
use warnings;
use Fcntl;
use Getopt::Long;
use POSIX;
use XML::Twig;

### UNTAINT ENVIRONMENT, SUPPLIED FILENAMES

#code to untaint env, filames here


my $twig;
my ($xmlfile, $ctlfile, $config);
my (@assm_header, @chain_header, @xmlfiles);
my %assm_header = ();
my %assm_line   = ();
my %pdb_line = ();
my %chains = ();
my %chain_header = ();

### HANDLE COMMAND LINE OPTIONS

# code to handle Getopt::long here

@xmlfiles = qw(file1.xml file2.xml);


foreach my $xfile (@xmlfiles)
{  

 $twig = new XML::Twig(
                         twig_roots =>  {
                        'pdb_entry/pdb_code' => \&pdb_entry,
                        'pdb_entry/total_asm' => \&pdb_entry,
                        'pdb_entry/asm_set/assembly' => \&assembly,});


   # &parse_twig($xfile); # sub code now inserted below

   ## sub code folded into here

   if ($twig->safe_parsefile($xfile) == 0)
   {
      die "Failed to parse $xfile: $@";
   }

   my $root = $twig->root;
   my @params = $root->children('pdb_entry');
   $twig->purge;
   $twig->dispose;

 }



...
 
handler code

    [download]

    result is file2 gets parsed and output, no sign of file1.. ;+(

[reply]
[d/l]
Re^2: parsing multiple xml files with xml::twig
by diomedea (Sexton) on Jun 08, 2007 at 13:36 UTC
    I have managed to get a workround by calling the parser from another program which feeds it one file at a time: 
    #! /usr/bin/perl 


use strict;
use warnings;
use Fcntl;
use Getopt::Long;
use POSIX;


my ($xmlfile, $ctlfile, $config);
my @xmlfiles;

### HANDLE COMMAND LINE OPTIONS

GetOptions('config|c=s'     => \$config,
           'ctlfile|ctl=s'  => \$ctlfile,
           'xmlfile|x=s'    => \$xmlfile,);


if ($xmlfile) # xmlfile specified on cmd line
{
   ($xmlfile = $1) = $xmlfile =~ /^(\w+\.*\w+)$/i;
    push @xmlfiles, $xmlfile;
}
elsif ($config) # xmlfiles in config file
{
   sysopen(XMLFILES, $config, O_RDONLY)
     or die "Can't open $config : $!";

   my @config = <XMLFILES>;
   foreach my $line (@config)
   {
      next if (($line =~ /^#+/) || ($line =~ /^\s+$/)) ;
      chomp($line);
      push @xmlfiles, $line;
   }
   close XMLFILES;
}
else  # try default filename then bale out
{
   $xmlfile = "multimers.pisa",  if (-e "multimers.pisa" and -s "multi
+mers.pisa");
   if ($xmlfile)
   {
      print "Using default xml file $xmlfile\n";
     ($xmlfile = $1) = $xmlfile =~ /^(\w+\.*\w+)$/i;
      push @xmlfiles, $xmlfile;
   }
   else
   {
      die "No valid xmlfile specified...exiting\n";
   }
}

foreach my $file (@xmlfiles)
{
   system "xml_pisa.pl $file"; # this calls the original              
+         
                               #  twig parsing script 
}

    [download]

[reply]
[d/l]

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