package PubMed::BaselineChange;

use strict;
use warnings;

use Carp qw(confess);
use File::Compare;
use File::Copy;
use File::Temp;
use Data::Dumper;

our $raw = sub {
  my $fufi=shift // "I need a file here.";
  my $blix=shift // "I need a blix here.";
  ## for real?
  my $real=shift // '';
  if(not $blix=~m|^\d{2}n$|) {
    confess "I don't like your blix '$blix'.";
  }
  my $tmp = File::Temp->new(UNLINK => 0);
  open(I,"< $fufi") or confess "I can't open $fufi.";
  my $line;
  while($line=<I>) {
    chomp $line;
    if($line=~m|^$blix\d+ \d+ \d+ \d+$|) {
      ## old line, to be skipped
      next;
    }
    print $tmp "$line\n";
  }
  $tmp->close;
  close I;
  my $tmp_filename=$tmp->filename();
  if(compare($fufi,$tmp_filename)==0) {
    print "$tmp_filename and $fufi are the same.\n";
    unlink $tmp_filename;
    return;
  }
  if(not $real) {
    print "I need to copy $tmp to $fufi but I will not do it.\n";    
    exit;
    #unlink $tmp;
    return;
  }
  print "I copy $tmp_filename to $fufi\n";    
  copy($tmp_filename,$fufi);
  unlink $tmp_filename;
};

our $sox = sub {
  my $fufi=shift // "I need a file here.";
  my $blix=shift // "I need a blix here.";
  ## for real?
  my $real=shift // '';
  if(not $blix=~m|^\d{2}n$|) {
    confess "I don't like your blix '$blix'.";
  }
  my $tmp = File::Temp->new(UNLINK => 0);
  my $tmp_filename=$tmp->filename();
  open(I,"< $fufi") or confess "I can't open $fufi.";
  my $line;
  while($line=<I>) {
    chomp $line;
    while($line=~m|( \d+ \d+ $blix\d+)|) {
      my $to_go=$1;
      $line=~s|$to_go||;
    }
    ## what remains? 
    if($line=~m|^\s*$|) {
      ## old line, to be skipped
      next;
    }
    ## added after the first run in 2015
    if($line=~m|^\d+$|) {
      ## old line, to be skipped
      next;
    }
    print $tmp "$line\n";
  }
  $tmp->close;
  close I;
  if(compare($fufi,$tmp_filename)==0) {
    print "$tmp_filename and $fufi are the same.\n";
    unlink $tmp;
    return;
  }
  if(not $real) {
    print "I need to copy $tmp to $fufi but I will not do it.\n";    
    exit;
    #unlink $tmp;
    return;
  }
  print "I copy $tmp to $fufi.\n";
  copy($tmp_filename,$fufi);
  unlink $tmp;
};

## removes bad pmids from dain
our $dain = sub {
  my $fufi=shift // confess "I need a file here.";
  my $gone_pmids=shift // confess "I need a gone_pmids hashref here.";
  my $ref_gone_pmids=ref $gone_pmids;
  if(not $ref_gone_pmids='HASH') {
    confess "I need a hashref here, not $ref_gone_pmids.";
  }
  ## for real?
  my $real=shift // '';
  my $tmp = File::Temp->new(UNLINK => 0);
  my $tmp_filename=$tmp->filename();
  open(I,"< $fufi") or confess "I can't open $fufi.";
  my $line;
  while($line=<I>) {
    chomp $line;
    if(not $line=~m|^(\d+)$|) {
      confess "bad line '$line'."
      #print $tmp "$line\n";
      #next;
    }
    my $pmid=$1;
    if(not defined($gone_pmids->{$pmid})) {
      print $tmp "$line\n";
      next;
    }
    ## if defined, we don't write
  }
  $tmp->close;
  close I;
  if(compare($fufi,$tmp_filename)==0) {
    print "$tmp_filename and $fufi are the same.\n";
    unlink $tmp;
    return;
  }
  if(not $real) {
    print "I need to copy $tmp to $fufi but I will not do it.\n";    
    exit;
    #unlink $tmp;
    return;
  }
  print "I copy $tmp_filename to $fufi.\n";
  copy($tmp_filename,$fufi);
  unlink $tmp;
};

  
1;