package PubMed::Common;

use strict;
use warnings;

use Carp qw(confess);
use Data::Dumper;
use File::Basename;
use XML::LibXML;
# use File::Temp;

sub pmid_to_pemi {
  my $num=shift;
  while(length($num)<3) {
    $num='0'.$num;
  }
  $num=substr($num,-3,3);
  return $num;
}

sub load_and_return_xml {
  my $file=shift;
  if (not -f $file) {
    confess "I have no such file $file";
  }
  my $fh;
  if($file=~m|\.gz$|) {
    open $fh , "/bin/gunzip -c $file |";
  }
  else {
    open $fh, '<', $file;
  }
  binmode $fh;
  my $doc;
  local $XML::LibXML::skipXMLDeclaration = 1;
  eval {
    $doc = XML::LibXML->load_xml(IO => $fh);
  };
  if(ref $doc ne 'XML::LibXML::Document') {
    confess "I could not parse file '$file'\nLibXML says $@\n";
  }
  return $doc;
}

sub get_pmid {
  my $meci=shift;
  my $ref_meci=ref $meci;
  if($ref_meci ne 'XML::LibXML::Element') {
    confess "I need an element, not a '$ref_meci'";
  }
  my $pmid_elements=$meci->getElementsByTagName('PMID');
  foreach my $pmid_element ($pmid_elements->get_nodelist()) {
    if($pmid_element->parentNode->nodeName eq 'MedlineCitation') {
      my $pmid=$pmid_element->textContent;
      if($pmid=~m|^\d+$|) {
        return $pmid;
      }
      confess "I have a bad pmid: '$pmid'";
    }
  }
  confess "I don't see a pmid in $meci";
}

sub isatty() {
  no autodie;
  my $tty;
  if(open($tty, '+<', '/dev/tty')) {
    close $tty;
    return 1;
  }
  return 0;
}

sub deal_with_files {
  my $dir=shift // confess "I need a directory here.";
  my $regx=shift // confess "I need a regx here.";
  my $fun_ref=shift // confess "I need a fun_ref here.";
  my $verbose=shift // confess "I need a verbosity parameter here.";
  # my $pat=shift // confess "I need a pattern here";
  my @args=@_;
  ## extra security
  my $real=shift // '';
  my $out={};
  foreach my $fufi (glob("$dir/*")) {
    my $bana=basename($fufi);
    if($regx and not $bana=~m|$regx|) {
      if($verbose) {
	print "I skip $bana, because it does not match '$regx'.\n";
      }
      next;
    }
    elsif($verbose) {
      print "I take $bana.\n";
    }
    my $fufi="$dir/$bana";
    if(not -f $fufi) {
      confess "I can't open $fufi";
    }
    $out->{$bana}=&{$fun_ref}($fufi,@args);
  }
  return $out;
}

1;