This is the code I am trying

$pidEmpty = pp($tree->{drug}->{$i}->{'general-references'}->{articles}
+->{article});
    if ($pidEmpty eq "undef") {
    
    }else{
    $pidArray = $tree->{drug}->{$i}->{'general-references'}->{articles
+}->{article};
    }
    if (ref($pidArray) eq "ARRAY"){
    for $y (@{$tree->{drug}->{$i}->{'general-references'}->{articles}-
+>{article}}){
    if ((ref($y) eq "HASH")){
    #print pp($y);
    #print "\n";
    $pid = $y->{'pubmed-id'};
    print "$pid\n";
    $pids = $pids . "$y,";
    }
    }
    }else{
    $pid = $pidArray->{'pubmed-id'};
    $pids = $pids . "$pid,";
    }
    $pids =~ s/,$//;
[download]

Doesnt help a bit. You havent shown us what modules you are using, where does pp() come from. you havent shown us where $tree or $i are assigned.

you may get a clue as to what is going on if you put these two statements before what you showed us.

use Data::Dumper; 
print Dumper($tree);
[download]

This is just a piece of code where I am getting this error. Below I have attached my code including all the models I have used.

use XML::Simple;
use Data::Dump "pp";
use Text::CSV;

my $csv = Text::CSV->new({ binary => 1, auto_diag => 1, eol => "\n"})
        or die "Cannot use CSV: " . Text::CSV->error_diag();

# open in append mode
open my $fh, ">>", "file1.csv" or die "Failed to open file: $!";

$csv->print($fh, [ "Drug Name", "Drug Bank ID", "Category", "Pubmed ID
+" ]);
#--close $fh;

@wantedcat = ("Blood", "Thrombus", "Thrombosis", "Anticoagulation", "C
+oagulation", "Anticoagulants", "Antithrombins");

my $simple = XML::Simple->new();
my $tree = $simple->XMLin('database-01.xml');
#print pp($tree);

$alldrug = $tree->{drug};
#print pp($alldrug);
@allkeys = keys %$alldrug;
#print scalar @allkeys;
for $i (@allkeys){
  #print $i;
  #print \n;
  @matchedcat = ();
  #if ($i eq "Cetuximab"){
  $isEmpty = pp($tree->{drug}->{$i}->{categories}->{category});
    if ($isEmpty eq "undef"){

    } else {
      $isArray = $tree->{drug}->{$i}->{categories}->{category};
      if (ref($isArray) eq "ARRAY"){
        for $o (@{$tree->{drug}->{$i}->{categories}->{category}}){
           #print pp($o);
           #print "\n";
          $cat = $o->{'category'};
          #print "$cat\n";
          for $i (@wantedcat){
            if ($cat eq $i){
              push(@matchedcat, $cat);
            }
          }
        }
      } else {
        #print "$i is HASH\n";
        #print pp($isArray);
        $cat = $isArray->{'category'};
        #print $cat;
          for $i (@wantedcat){
            if ($cat eq $i){
              push(@matchedcat, $cat);
            }
          }
      }

      #print scalar @matchedcat;
      if (scalar @matchedcat > 0){
        $count = $count + 1;
        $name = $i;
        #print "$name \n";
        $category = "";
        for $x (@matchedcat){
          $category = $category . "$x,";
        }
        $category =~ s/,$//;
        #print "$category\n";

        # ### --- print all IDs of drug
        $ids = "";
    $pids = "";
        $idArray = $tree->{drug}->{$i}->{'drugbank-id'};

        if (ref($idArray) eq "ARRAY"){
          for my $s (@{$tree->{drug}->{$i}->{'drugbank-id'}}){
            if ((ref($s) eq "HASH")){
              $id = pp($s->{'content'});
              $id =~ s/"//g;
              #print $id;
              #print "\n";
              $ids = $ids . "$id,";
            } else {
              #print $s;
              #print "\n";
              $ids = $ids . "$s,";
            }
          }
        } else {
          #print pp($idArray);
          $id = pp($idArray->{'content'});
          $id =~ s/"//g;
          $ids = $ids . "$id,";
        }
        $ids =~ s/,$//;
        #print $ids;
        #print "\n --- THE END --- \n";

    $pidEmpty = pp($tree->{drug}->{$i}->{'general-references'}->{artic
+les}->{article});
    if ($pidEmpty eq "undef") {
    
    }else{
        $pidArray = $tree->{drug}->{$i}->{'general-references'}->{arti
+cles}->{article};
    }
    if (ref($pidArray) eq "ARRAY"){
        for $y (@{$tree->{drug}->{$i}->{'general-references'}->{articl
+es}->{article}}){
            #if ((ref($y) eq "HASH")){
                #print pp($y);
                #print "\n";
                $pid = $y->{'pubmed-id'};
                print "$pid\n";
                $pids = $pids . "$y,";
                #}
            }
            }else{
                $pid = $pidArray->{'pubmed-id'};
                $pids = $pids . "$pid,";
                }
            $pids =~ s/,$//;
    
    

        #print $name, $ids, $category, $pids;
        #open my $fh, ">>", "$file1.csv" or die "Failed to open file: 
+$!";
        $csv->print($fh, [ $name, $ids, $category, $pids]);
        #close $fh;
      }
    }
  

}
print "DONE.";

close $fh;
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