in reply to Re: XML::TreeBuilder capture multiple attributes to array
in thread XML::TreeBuilder capture multiple attributes to array

The issue is I asked a colleague for advise whilst waiting for a reply from that thread and as a result my most complete script is all written to use TreeBuilder now. I would have the same problem if I used Twig I feel. I just need it to return 1, 2, 3 etc. After writing 5 scripts, doing some serious googling and pestering colleagues via email I still can't get it to work. Google results show examples where people have used the above example or:

@array = $drug->find_by_tag_name('groups')->find_by_tag_name('group')->as_text;

But I can't get this to capture all the information I need. Getting very fed up and disheartened so whoever helps me out should know in advance they're doing their super good deed of the day!

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Re^3: XML::TreeBuilder capture multiple attributes to array
by toolic (Bishop) on Jul 05, 2012 at 14:20 UTC
    You could do your "super good deed of the day" by posting:
    • Legal XML code: you have no closing drug tag and mismatched target/targets tags.
    • Perl code which shows how you construct your TreeBuilder object and call the parse method.
    By posting an incomplete question you are likely to get incomplete answers.
[reply]

      OOPS sorry again! That XML still incomplete, this is correct now:

      <drug type="small molecule">
  <name>Goserelin</name>
  <targets>
      <target partner="1">
      <known-action>yes</known-action>
      </target>
      <target partner="2">
      <known-action>yes</known-action>
      </target>
      <target partner="3">
      <known-action>yes</known-action>
      </target>
  </target>
</drug>

      [download]

      Here's the complete Perl script, which just got deleted when I updated:

      use XML::TreeBuilder;

my $file = $ARGV[0];
my $tree = XML::TreeBuilder->new();
$tree->parse_file($file);

foreach my $drug ($tree->find_by_tag_name('drug')){

my @targets = $drug->look_down ('_tag', 'targets')->look_down ('_tag',
+ 'target')->attr_get_i('partner');

foreach my $id (@targets){print "\t$id";}

my @actions = $drug->look_down ('_tag', 'targets')->look_down ('_tag',
+ 'known-action')->as_text;

foreach my $act (@actions){print "\t$act";}

}

      [download]

      And also because I updated I think all my apologising is gone, so just to summarise: I'm sorry for how that came across, I was just trying to let people know that I really do appreciate the help a lot

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        Broken XML again :|

        Also broken, XML::TreeBuilder/XML::Element/attr_get_i

        This works 

        #!/usr/bin/perl --
use strict; use warnings;
use Data::Dump;
use XML::TreeBuilder;

my $tree = XML::TreeBuilder->new();
$tree->parse(<<'__XML__');
<drug type="small molecule">
  <name>Goserelin</name>
  <targets>
    <target partner="1">
      <known-action>yes</known-action>
    </target>
    <target partner="2">
      <known-action>yes</known-action>
    </target>
    <target partner="3">
      <known-action>yes</known-action>
    </target>
  </targets>
</drug>
__XML__


foreach my $drug ( $tree->find_by_tag_name('drug') ) {
    
    my @targets = $drug->look_down( '_tag', 'target' );
    for my $target ( @targets ){
        print $target->attr('partner'), "\t";
    }

    print "\n";
    
    my @act = $drug->look_down( '_tag', 'known-action' );
    @act = map { $_->as_trimmed_text } @act;
    
    print join "\t", @act, "\n";
    
}

        [download]
[reply]
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